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The tree of life, common descent, common ancestry, a failed hypothesis

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The tree of life, common descent, common ancestry, a failed hypothesis

http://reasonandscience.heavenforum.org/t2239-the-tree-of-life-common-descent-common-ancestry-a-failed-hypothesis

As of 2014, Koonin serves on the advisory editorial board of Trends in Genetics, and is co-Editor-in-Chief of the open access journal Biology Direct. He served on the editorial board of Bioinformatics from 1999-2001. Koonin is also an advisory board member in bioinformatics at Faculty of 1000.

Koonin, the logic of chance, page 214:
Arguments for a LUCA that would be indistinguishable from a modern prokaryotic cell have been presented, along with scenarios depicting LUCA as a much more primitive entity (Glansdorff, et al., 2008).
The difficulty of the problem cannot be overestimated. Indeed, all known cells are complex and elaborately organized. The simplest known cellular life forms, the bacterial (and the only known archaeal) parasites and symbionts, clearly evolved by degradation of more complex organisms; however, even these possess several hundred genes that encode the components of a fully fledged membrane; the replication, transcription, and translation machineries; a complex cell-division apparatus; and at least some central metabolic pathways. As we have already discussed, the simplest free-living cells are considerably more complex than this, with at least 1,300 genes. 

All the difficulties and uncertainties of evolutionary reconstructions notwithstanding, parsimony analysis combined with less formal efforts on the reconstruction of the deep past of particular functional systems leaves no serious doubts that LUCA already possessed at least several hundred genes.  In addition to the aforementioned “golden 100” genes involved in expression, this diverse gene complement consists of numerous metabolic enzymes, including pathways of the central energy metabolism and the biosynthesis of amino acids, nucleotides, and some coenzymes, as well as some crucial membrane proteins, such as the subunits of the signal recognition particle (SRP) and the H+- ATPase.

The reconstructed gene repertoire of LUCA also has gaping holes. The two most shocking ones are

(i) the absence of the key components of the DNA replication machinery, namely the polymerases that are responsible for the initiation (primases) and elongation of DNA replication and for gap-filling after primer removal, and the principal DNA helicases (Leipe, et al., 1999), and
(ii) the absence of most enzymes of lipid biosynthesis. These essential proteins fail to make it into the reconstructed gene repertoire of LUCA because the respective processes in bacteria, on one hand, and archaea, on the other hand, are catalyzed by different, unrelated enzymes and, in the case of membrane phospholipids, yield chemically distinct membranes.

bacteria and archaea have membranes made of water-repellent fatty molecules. Simple fatty molecules tend to flip around, making the membrane leaky, so both bacteria and archaea tacked on a water-loving phosphate group to stabilise the molecules and make their membranes impermeable. They took very different routes, though. Bacterial membranes are made of fatty acids bound to the phosphate group while archaeal membranes are made of isoprenes bonded to phosphate in a different way. This suggests that their membranes evolved independently. This leads to something of a paradox: if LUCA already had an impermeable membrane for exploiting proton gradients, why would its descendants have independently evolved two different kinds of impermeable membrane? 17

My remark:

Schocking and remarkable indeed :
The DNA replication machinery is essential in all domains, and so is lipid biosynthesis for cell membranes. Its not possible that the first cells emerged without membranes and DNA replication in a LUCA, and then evolved distinguished membranes and DNA replication, each by its own.


That means,  the at least several hundred genes possessed in all tree domains of life would have had to emerge in a convergent manner ( that is separately they would have come into existence with the same genome, proteome and metabolome except  lipid biosynthesis and DNA replication which  were the two only distinct parts that diverged each from the other domains. This is a hard sell when evoking evolution. Even more when only unguided random mechanisms were at hand, that is chance and luck. If the emergency of one cell type would have been exceedingly improbable, imagine the same feat tree separate times. As Stephen J. Gould wrote in Wonderful Life: The Burgess Shale and the Nature of History :

“…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.1

Neither a LUCA is credible, nor naturally emerging tree separate domains of life through  partially  convergent manner. The only rational explanation is a designer creating the tree domains of life separately, and using the same toolkit where required, and a separate divergent toolkit for other parts.

Should that not be evidence that a LUCA never existed, and that the three domains of life had to emerge separately through a intelligent designer ? 


The widespread role of non-enzymatic reactions in cellular metabolism
Sequences of glycolytic enzymes differ between Archaea and Bacteria/Eukaryotes 14 
LUCA helloo....

Evolution of the coordinate regulation of glycolytic enzyme genes by hypoxia
There is no evidence of a common ancestor for any of the four glycolytic kinases or of the seven enzymes that bind nucleotides 15


Genetic, protein and DNA analysis, together with major differences in the biochemistry and molecular biology of between all three domains – Bacteria, Archaea and Eukaryota – suggest that the three fundamental cell types are distinct and evolved separately (i.e. Bacteria are not actually pro-precursors of the eukaryotes, which have sequence similarities in particular parts of their biochemistry between both Bacteria or Archaea).  Only a relatively small percentage of genes in Archaea have sequence similarity to genes in Bacteria or Eukaryota. Furthermore, most of the cellular events triggered by intracellular Ca2+ in eukaryotes do not occur in either Bacteria or Archaea.

Prokaryotic evolution and the tree of life are two different things
The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761302/

The network of life: genome beginnings and evolution
The rapid growth of genome-sequence data since the mid-1990s is now providing unprecedented detail on the genetic basis of life, and not surprisingly is catalysing the most fundamental re-evaluation of origins and evolution since Darwin’s day. Several papers in this theme issue argue that Darwin’s tree of life is now best seen as an approximation—one quite adequate as a description of some parts of the living world (e.g. morphologically complex eukaryotes), but less helpful elsewhere (e.g. viruses and many prokaryotes); indeed, one of our authors goes farther, proclaiming the “demise” of Darwin’s tree as a hypothesis on the diversity and seeming naturalness of hierarchical arrangements of groups of living organisms.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874017/

Uprooting the Tree of Life
Charles Darwin contended more than a century ago that all modern species diverged from a more limited set of ancestral groups, which themselves evolved from still fewer progenitors and so on back to the beginning of life. In principle, then, the relationships among all living and extinct organisms could be represented as a single genealogical tree.Most contemporary researchers agree. Many would even argue that the general features of this tree are already known, all the way down to the root—a solitary cell, termed life’s last universal common ancestor, that lived roughly 3.5 to 3.8 billion years ago. The consensus view did not come easily but has been widely accepted for more than a decade. Yet ill winds are blowing. To everyone’s surprise, discoveries made in the past few years have begun to cast serious doubt on some aspects of the tree, especially on the depiction of the relationships near the root.
http://labs.icb.ufmg.br/lbem/aulas/grad/evol/treeoflife-complexcells.pdf


http://youngearth.com/marine-worm-infects-trunk-darwins-tree-be-felled-soon

marine worms are more closely related to humans than are mollusks and insects - Nature 2-9-11

Newly Discovered 'Orphan Genes' Defy Evolution 2

An important category of "rogue" genetic data that utterly defies evolutionary predictions is the common occurrence of taxonomically restricted genes, otherwise known as "orphan genes." These are now being discovered in the sequencing of all genomes.

Many multicellular animals share similar sets of genes that produce proteins that perform related biochemical functions. This is a common feature of purposefully engineered systems. In addition to these standard genes, all organisms thus far tested also have unique sets of genes specific to that type of creature.

The authors of a recent review paper, published in Trends in Genetics, on the subject of orphan genes stated, "Comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs [similar counterparts] in other species."1

These orphan genes are also being found to be particularly important for specific biological adaptations that correspond with ecological niches in relation to the creature's interaction with its environment.2 The problem for the evolutionary model of animal origins is the fact that these DNA sequences appear suddenly and fully functional without any trace of evolutionary ancestry (DNA sequence precursors in other seemingly related organisms). And several new studies in both fish and insect genomes are now highlighting this important fact.

What Is the Tree of Life?
A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic. 12  One of the several ways in which microbiology puts the neo-Darwinian synthesis in jeopardy is by the threatening to “uproot the Tree of Life (TOL)” [1]. Lateral gene transfer (LGT) is much more frequent than most biologists would have imagined up until about 20 years ago, so phylogenetic trees based on sequences of different prokaryotic genes are often different. How to tease out from such conflicting data something that might correspond to a single, universal Tree of Life becomes problematic. Moreover, since many important evolutionary transitions involve lineage fusions at one level or another, the aptness of a tree (a pattern of successive bifurcations) as a summary of life’s history is uncertain [2–4].
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005912

Octopuses ‘are aliens’, scientists decide after DNA study 
http://metro.co.uk/2015/08/12/octopuses-are-aliens-scientists-decide-after-dna-study-5339123/

Not to freak you out or anything, but scientists have just revealed that octopuses are so weird they’re basically aliens.
The first full genome sequence shows of that octopuses (NOT octopi) are totally different from all other animals – and their genome shows a striking level of complexity with 33,000 protein-coding genes identified, more than in a human.
There we were thinking it was quite freaky enough when they learned how to open jam jars.
US researcher Dr Clifton Ragsdale, from the University of Chicago, said: ;The octopus appears to be utterly different from all other animals, even other molluscs, with its eight prehensile arms, its large brain and its clever problem-solving abilities.
‘The late British zoologist Martin Wells said the octopus is an alien. In this sense, then, our paper describes the first sequenced genome from an alien.’
Octopuses: What even ARE they?
They inhabit every ocean at almost all depths and possess a range of features that call to mind sci-fi aliens.
These include prehensile sucker-lined tentacles, highly mobile, camera-like eyes sensitive to polarised light, sophisticated camouflage systems that alter skin colour and patterns, jet-propulsion, three hearts, and the ability to regenerate severed limbs.
The scientists estimate that the two-spot octopus genome contains 2.7 billion base pairs – the chemical units of DNA – with long stretches of repeated sequences.

Octopus Have Been Found to have Unique Genes
http://www.natureworldnews.com/articles/16161/20150820/octopus-found-unique-genes.htm
hundreds of other genes that are common in cephalopods, but unknown in other animals, were found.

Decoding the genome of an alien
https://www.eurekalert.org/pub_releases/2015-08/oios-dtg081215.php
Besides recognizable genes, vast swathes of the genome consist of regulatory networks that control how genes are expressed in cells. In the octopus, nearly half of the genome was found to be composed of mobile elements called transposons, one of the highest proportions in the animal kingdom. Transposons replicate and move around with a life of their own, disrupting or enhancing gene expression and facilitating reshufflings of gene order. The researchers found many of them to be particularly active in the octopus nervous system. The "Hox" genes, involved in embryonic development in all animals, are a particularly dramatic example. Although clustered together in most animals, including other mollusks, they are scattered in snippets in the octopus, presumably enabling the evolution of the versatile cephalopod body plan.

Presumably. Yes. Or , in other words, guess work as always......  The architecture of a body plan must be right from the beginning. Everything goes, or nothing goes. The question is, where does the information of this reshuffling of genes came from ? In my view, the only rational explanation is intentional design.

Are Rotifers Gene Stealers or Uniquely Engineered? 1

The tools of DNA sequencing are becoming cheaper to use and more productive than ever, and the deluge of DNA comparison results between organisms coming forth are becoming a quagmire for the evolutionary paradigm. To prop it up, biologists resort to ever more absurd explanations for discrepancies. A prime example of this trickery is in a recent DNA sequencing project performed in a microscopic aquatic multi-cellular animal called a rotifer.1
In this effort, the researchers targeted those gene sequences that are expressed as proteins for DNA sequencing because the genome was too large and complex to sequence and assemble all of its DNA. They recorded over 61,000 gene sequences that were expressed from rotifers grown in stressed and non-stressed conditions. Of these, they could only find sequence similarities between rotifers and other creatures for 28,922 sequences (less than half). The researchers tossed the unknown DNA sequences out of their analysis since the non-similar genes were novel, apparently specific to rotifer, and essentially difficult for evolution to explain.
Of the 28,922 sequences for which they could obtain a match in a public database of other creature's DNA and protein sequences, a significant proportion (more than in any other creature sequenced) did not fit evolutionary expectations of common descent. Further complicating this picture, the rotifer gene sequences were found in a diverse number of non-rotifer creatures! Some of the creatures that had gene matches to rotifers included a variety of plants, other multicellular animals, protists (complex single celled animals), archaea, bacteria, and fungi. Evolutionists have two options in which to categorize these unusual gene matches based on their naturalistic presuppositions. First, they can say that these genes evolved independently in separate creatures in a hypothetical process called "convergent evolution." However, in cases where there are literally hundreds of these DNA sequences popping up in multiple organisms, this scenario becomes so unlikely that even evolutionists have too much difficulty imagining it. The second option is called "horizontal gene transfer," or HGT. This involves the transfer of genes, perhaps via some sort of microbial host vector such as a bacterium.2

What a bust against common ancestry from a mainstream scientist :

The Biological Big Bang model for the major transitions in evolution
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1973067/

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal.

The argument of the broken down evolution tree  
1. The fundamental tenet of evolution theory is that species evolved according to the evolutionary tree; one after the other evolved, as a genealogical family tree.
2. However, since Darwin, science has continued to document exceptions and anomalies—species that don’t fit neatly into the evolutionary pattern.
-- For example, species that in many regards appear to be quite similar, which evolutionists have placed on neighboring twigs of the evolutionary tree, are routinely found to have profound differences. Here is an example:
a. In 2010 an article in the journal Nature[4] released the results of a human-chimp DNA study with implications that was very surprising for the scientific community because the result of the research contradicted the long-held hypothesis of their similarity.
b. Already the title summed up the research findings: "Chimpanzee and Human Y Chromosomes are Remarkably Divergent in Structure and Gene Content."
c. The chimpanzee DNA sequence for a chromosome was assembled and oriented based on a Y chromosome map/framework built for chimpanzee and not human. As a result, the chimpanzee DNA sequence could then be more accurately compared to the human Y chromosome.
d. The chimp and human Y chromosomes had a dramatic difference in gene content of 53 percent. In other words, the chimp was lacking approximately half of the genes found on a human Y chromosome.
c. The researchers also sought to determine if there was any difference in actual gene categories and they found a shocking 33 percent difference.
e. The human Y chromosome contains a third more gene categories--entirely different classes of genes--compared to chimps.
f. Because virtually every structural aspect of the human and chimp Y chromosomes was different, it was hard to arrive at an overall similarity estimate between the two. The researchers did postulate an overall 70 percent similarity, which did not take into account size differences or structural arrangement differences. This was done by concluding that only 70 percent of the chimp sequence could be aligned with the human sequence--not taking into account differences within the alignments. I.O.W. 70 percent was a conservative estimate, especially when considering that 50 percent of the human genes were missing from the chimp, and that the regions that did have some similarity were located in completely different patterns. When all aspects of non-similarity--sequence categories, genes, gene families, and gene position--are taken into account, it is safe to say that the overall similarity was lower than 70 percent.
g. The Nature article we can read, "Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation."
h. So, the human Y chromosome looks just as different from a chimp as the other human chromosomes do from a chicken. And to explain where all these differences between humans and chimps came from, believers in big-picture evolution are forced to invent stories of major chromosomal rearrangements and rapid generation of vast amounts of many new genes, along with accompanying regulatory DNA.
i. However, since each respective Y chromosome appears fully integrated and interdependently stable with its host organism, the most logical inference from the Y chromosome data is that humans and chimpanzees were each specially created as distinct creatures.
-- On the other hand, species that are obviously quite different, which evolutionists have placed on distant limbs of the evolutionary tree, are often found to have profound similarities.
a. Humans, Arabidopsis (A genus of the mustard-family having white, yellow or purplish flowers), and nematodes (Unsegmented worms with elongated rounded body pointed at both ends) all have about the same number of genes.
a. A research team from Heidelberg from the European Molecular Biology Laboratory [EMBL][1], compared human and fruit-fly introns[2] with those of a roundworm thought to be 600 million years old. Surprisingly, introns were already in the worms from the beginning of their appearance and remained the same all the way to the human line, changing rapidly and losing many of them only in other species like insects. One of the researchers remarked, “Now we have direct evidence that genes were already quite complex in the first animals, and many invertebrates have reduced part of this complexity.” Yet another said, “The worm’s genes are very similar to human genes…That’s a much different picture than we’ve seen from the quickly-evolving species that have been studied so far.” Additionally, the genome too “has been preserved over the last half a billion years.” In their research they did not explain how the early-Cambrian roundworms got their complexity and ability to remain unchanged for millions of years. The discovery is obviously changing the evolution tree.
b. Molecular evolution trees often do not fit a morphology-based evolution tree. For example, there are several TRAF genes in humans and Drosophila, and obvious prediction of Darwin’s model is that there must be an ancestral gene in a common ancestral organism from which the modern TRAF genes were derived. In reality, however, a TRAF gene from Hydra does not fit criteria of an ancestral gene, which must be somewhat of a mix of all human TRAF families, but rather clearly belongs to the major group of TRAF genes along with human TRAF1, TRAF2, TRAF3 and TRAF 5, while human TRAF4 and especially TRAF6 belong to different groups together with Drosophila TRAFs. [3]
3. For years evolutionists attempted to explain the growing list of contradictions using their evolutionary tree model. But it is obvious that this was an exercise in forcing the evidence to fit the theory rather than the other way around.
4. In recent years evolutionists have finally begun to deemphasize their iconic evolutionary tree model. What this does not change, however, is their insistence that evolution is a fact.
5. Thus, even nowadays students are taught that the species fall into the expected tree pattern. But some venturesome writers are beginning to mention this unmentionable, foridden archeology.
6. Few years ago, for instance, the Telegraph reported that “Charles Darwin's tree of life is ‘wrong and misleading.’
-- They believe the concept misleads us because his [Darwin’s] theory limits and even obscures the study of organisms and their ancestries. …
-- Researchers say although for much of the past 150 years biology has largely concerned itself with filling in the details of the tree it is now obsolete and needs to be discarded. …
-- “For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality.” …
-- More fundamentally recent research suggests the evolution of animals and plants isn't exactly tree-like either. …
-- Dr Rose said: "The tree of life is being politely buried – we all know that. What's less accepted is our whole fundamental view of biology needs to change." He says biology is vastly more complex than we thought and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century.
7. Contrary evidences were/are continuously openly discussed. But none of them is allowed to cast any doubt on evolutionary theory itself. As the article reported:
8. "If you don't have a tree of life what does it mean for evolutionary biology? At first it's very scary – but in the past couple of years people have begun to free their minds." Both he and co-researcher Dr Ford Doolittle stressed that downgrading the tree of life doesn't mean the theory of evolution is wrong just that evolution is not as tidy as we would like to believe.
9. The theory has to be repeatedly modified and augmented to try to fit the data. At some point the theory becomes little more than a tautology. Namely, whatever discovery is made in biology, evolution must have created it, no matter how contradictory and unlikely.
10. However such tautology is one of the fallacies in logic. By definition:
"Tautology in formal logic refers to a statement that must be true in every interpretation by its very construction. In rhetorical logic, it is an argument that utilizes circular reasoning, which means that the conclusion is also its own premise. Typically the premise is simply restated in the conclusion, without adding additional information or clarification. The structure of such arguments is A=B therefore A=B, although the premise and conclusion might be formulated differently so it is not immediately apparent as such."
11. Thus the only logical explanation of differences between similar species and similarities of different species is an involvement of an intelligent designer using similar genetic patterns. This all men call God.
12. God exists.

Notes:
1. Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii F. Raible, K. Tessmar-Raible, K. Osoegawa, P. Wincker, C. Jubin, G. Balavoine, D. Ferrier, V. Benes, P. de Jong, J. Weissenbach, P. Bork and D. Arendt.
2. intron - Part of a gene whose sequence is transcribed but not present in a mature mRNA after splicing.
3. Mali B, Frank U. Hydroid TNF-receptor-associated factor (TRAF) and its splice variant: a role in development.Mol Immunol. (2004) 41:377-84
4. Hughes, J.F. et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure gene content. Nature. 463 (7280): 536-539.


At about the same time, Dalhousie University evolutionary biologist W. Ford Doolittle concluded that lateral gene transfer among ancient organisms meant that molecular phylogeny might never be able to discover the “true tree” of life, not because it is using the wrong methods or the wrong genes, “but because the history of life cannot properly be represented as a tree.” He concluded: “Perhaps it would be easier, and in the long run more productive, to abandon the attempt to force” the molecular data “into the mold provided by Darwin.” Instead of a tree, Doolittle proposed “a web- or net-like pattern.” 10

The controversy over the universal tree of life continues. In 2002, Woese suggested that biology should go beyond Darwin’s doctrine of common descent. In 2004, he wrote: “The root of the universal tree is an artifact resulting from forcing the evolutionary course into a tree representation when that representation is inappropriate.” In 2004, Doolittle and his colleagues proposed replacing the tree of life with a net-like “synthesis of life,” and in 2005 they recommended that “representations other than a tree should be investigated.” Meanwhile, other scientists continue to defend the hypothesis that the universal ancestor existed but was complex rather than simple 11

“DR ROSE SAID: ‘THE TREE OF LIFE IS BEING POLITELY BURIED – WE ALL KNOW THAT. WHAT’S LESS ACCEPTED IS OUR WHOLE FUNDAMENTAL VIEW OF BIOLOGY NEEDS
TO CHANGE.’ HE SAYS BIOLOGY IS VASTLY MORE COMPLEX THAN WE THOUGHT AND FACING UP TO THIS COMPLEXITY WILL BE AS SCARY AS THE CONCEPTUAL UPHEAVALS PHYSICISTS HAD TO TAKE ON BOARD IN THE EARLY 20TH CENTURY.”


The Rooting of the Universal Tree of Life Is Not Reliable 5

Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria–Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.

Early evolution without a tree of life 6

There is more to evolution than will fit on any tree. For understanding major transitions in early evolution, we might not need a tree of life at all. But we need to keep our ideas testable with data from genomes or other independent data so as to keep our nose pinned to the grindstone of observations. The very early evolution of life is mostly written in the language of chemistry, some of which is (arguably) still operating today in modern metabolism if we look at the right groups . The environments and starting material that the Earth had to offer to fuel early chemistry are variables that only geochemists can reasonably constrain . One can make a case that acetogens (clostridial firmicutes) and hydrogenotrophic methanogens (euryarchareotes) harbour the ancestral states of microbial physiology in the eubacteria and archaebacteria respectively , and some trees are compatible with that view , as is the distribution of primitive energy-conserving mechanisms . But given a transition from the elements on early Earth to replicating cells, the course of prokaryote evolution does not appear to play out along the branches of a phylogenetic tree. For example, Whitman surveyed the biology and diversity of prokaryotes, showing an rRNA tree to discuss matters of classification; but branching orders in that tree play no role in his discussion of diversity or underlying evolutionary processes. If that is the direction we are headed , it is not all bad. But having the eukaryotes sitting on one branch in the rRNA tree of life rather than on two, as they should be (or three in the case of plants with their plastids), is far enough off the mark that we should be striving for a better representation of the relationship of eukaryotes to the two kinds of prokaryotes from which they stem.

Eukaryotes are genetic chimaeras and the role of mitochondria in the origin of that chimaerism is apparent . Eukaryotes are complex and the pivotal role of mitochondria in the origin of that complexity (as opposed to a pivotal role of phagocytosis) seems increasingly difficult to dispute, for energetic reasons . That leaves little reasonable alternative to the view that the host for the origin of mitochondria was a prokaryote, in the simplest of competing alternatives an archaebacterium . The antiquity of anaerobic energy metabolism and sulfide metabolism among eukaryotes meshes well with newer views of Proterozoic ocean chemistry . A challenge remains in computing networks of genomes that include lateral gene transfers among prokaryotes and the origin of eukaryotes in the same graph. Tracking early evolution without a tree of life affords far more freedom to explore ideas than thinking with a tree in hand. The ideas need to generate predictions and be testable, though, otherwise they are not science. If we check our thoughts too quickly against a tree whose truth nobody can determine anyway, the tree begins to decide which thoughts we may or may not have and which words we may or may not use. Should a tree of life police our thoughts? Working without one is an option.

Pattern pluralism and the Tree of Life hypothesis 7

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or fordifferent purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.

A Common Evolutionary Origin for Tailed-Bacteriophage Functional Modules and Bacterial Machineries  8

The dramatic divergence of bacteriophage genomes is an obstacle that frequently prevents the detection of homology between proteins and, thus, the determination of phylogenetic links between phages. For instance, sequence similarity between Siphoviridae major tail proteins (MTPs), which have been experimentally demonstrated to form the phage tail tube, is often not detectable

The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage 9

Phage do not contain a ribosomal sequence that allows them to be placed on the universal tree of life and, to date, have not benefited from their own gene-based taxonomic system. Previous attempts to classify and measure phage biodiversity based on genetic markers have met with limited success. Although structural proteins (e.g., capsids) could hypothetically serve as a basis for phage taxonomy (27, 29, 41, 60), they are highly diverse and, unlike rDNAs, do not contain conserved regions that allow them to be easily identified. This limits the usefulness of these proteins as markers for biodiversity studies. We show here that no single gene is found in all phage that can be used as the basis for a classification system.

What Exactly Does Genetic Similarity Demonstrate? 1

Origin of genes with unresolved ancestry

The Main Issue: Unintelligent vs. Intelligent Mechanism

My hope is that one day thinking about Darwinian Theory will become clearer in the public square. Recall that Darwin made two claims: (1) all living beings descend from one or a few original ancestors, and (2) the mechanism driving the changes among species is the blind, unguided mechanism of natural selection.

The controversial claim, of course, is the second one--the idea that a purely material mechanism, without any intelligence involved, is responsible for all of the genetic information necessary for life (DNA) and hence for all of life's diversity.


Sequence Similarity Alone Does NOT Prove Common Ancestry

the 98.8% DNA sequence similarity between chimps and humans that Clines references does not even establish claim one (common ancestry). And "you don't have to take my word for it," as LeVar Burton always used to say on Reading Rainbow.

As Francis Collins, head of the project which mapped the human genome, has written of DNA sequence similarities
"This evidence alone does not, of course, prove a common ancestor" because an intelligent cause can reuse successful design principles.


We know this because we are intelligent agents ourselves, and we do this all the time. We take instructions we have written for one thing and use them for another. The similarity is not the result of a blind mechanism but rather the result of our intelligent activity.

Some design proponents think the evidence for common ancestry is good (e.g., Michael Behe), while others--citing the fossil record, especially The Cambrian Explosion--do not. But neither group thinks that sequence similarity alone proves either common ancestry or the Darwinian mechanism, as so many science writers of our day seem eager to assume.

More than just orphans: are taxonomically-restricted genes important in evolution? 2

Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes.


Similarities between living organisms could be because they have been designed by the same intelligence, just as we can recognize a Norman Foster building by his characteristic style , or a painting by Van Gogh. 3 We expect to see repeated motifs and re-used techniques in different works by the same artist/designer.

In addition, similarities can be interpreted as evidence for design economy. Why should a designer come up with, for example, a new system of genetic code for each type of organism? Why should basic metabolic pathways or the universal energy currency differ between organisms? They do not need to because an intelligent designer can build diversity around common features.

Part of the reason for similarity in design, is that organisms have similar demands placed upon them, which can only be met in a limited number of ways. All cars have wheels, not because they have evolved from each other, but because the car designing community recognizes wheels as an efficient way of moving over a flat surface. In the same way there are limited ways of respiring, photosynthesizing or transporting energy.

Dissimilarities

If similarity is evidence for common ancestry, then does its opposite – dissimilarity – provide evidence against common ancestry?

There is, of course, much dissimilarity between living organisms, some of these at a very fundamental level. For example, the standard system of genetic code used by humans is not universal. Eighteen different genetic codes have been found in various species. Many scientists see this as evidence that all life does not come from a single common ancestor.

Similar genes and proteins in organisms are taken as evidence for common ancestry. But :

as we sequence more and more genomes, we repeatedly find genes which are unique to organisms. These are known as ORFans, and provide a real conundrum for evolutionists.

The DNA sequences of humans and chimpanzees are 96% similar, but the 4% difference represents 40 million individual differences at the nucleotide level.

When genes and proteins are used to try to reconstruct the ancestry of different organisms, and how they are linked in a tree-like pattern, different sources of evidence give different results. Different genes and proteins have conflicting patterns of similarity and difference between organisms. Evolutionists can only get round this problem by working out the most efficient way in which evolution could have worked. When they do this, they have to come up with scenarios where some similarities between organisms are not due to common ancestry, but to convergent evolution. This raises another problem: if similarities are not always due to common ancestry, how can they be evidence for common ancestry?

If the living world is designed, the patterns of similarity and difference we see in the living world could be due to selective use of designed modules to produce different combinations of features.

Comparative biochemistry and cell biology does not give clear evidence for macro-evolution. In fact, recent discoveries such as the non-universality of the genetic code are strong arguments against common ancestry. The patterns of similarity and difference in living organisms are fully consistent with design.


Common DNA Sequences: Evidence of Evolution or Efficient Design?


With the advent of modern biotechnology, researchers have been able to determine the actual sequence of the roughly three billion bases of DNA (A,T,C,G) that make up the human genome. They have sequenced the genomes of many other types of creatures as well. Scientists have tried to use this new DNA data to find similarities in the DNA sequences of creatures that are supposedly related through evolutionary descent, but do genetic similarities provide evidence for evolution?

DNA Supports Distinct Kinds

In the June 2009 Acts & Facts, an article was published by the author that showed how this approach has been used in an attempt to demonstrate an evolutionary relationship between humans and chimpanzees.1 The article showed that scientists incorporate a large amount of bias in their analyses in order to manipulate the data to support evolution, when in fact the DNA data support the obvious and distinctive categorization of life that is commonly observed in the fossil record and in existing life forms.

In reality, there is a clear demarcation between each created kind (humans, chimps, mice, chickens, dogs, etc.), and there is no blending together or observed transition from one kind of animal to another. All created kinds exhibit a certain amount of genetic variability within their grouping while still maintaining specific genetic boundaries. In other words, one kind does not change into another, either in the fossil record or in observations of living organisms.

Similar DNA Sequences


While the genome of each created kind is unique, many animal kinds share some specific types of genes that are generally similar in DNA sequence. When comparing DNA sequences between animal taxa, evolutionary scientists often hand-select the genes that are commonly shared and more similar (conserved), while giving less attention to categories of DNA sequence that are dissimilar. One result of this approach is that comparing the more conserved sequences allows the scientists to include more animal taxa in their analysis, giving a broader data set so they can propose a larger evolutionary tree.

Although these types of genes can be easily aligned and compared, the overall approach is biased towards evolution. It also avoids the majority of genes and sequences that would give a better understanding of DNA similarity concepts.

Tumor Suppressor Genes

As an example, there is a group of genes that not only have been used in evolutionary studies, but also have a significant impact on human health: the tumor suppressor genes. Aberrations within tumor suppressor genes can lead to cancer, thus it is important that their sequences remain unaltered. These genes tend to be very similar across many types of animals, making them ideal for comparative purposes. The close similarities of these genes between many animal taxa have led to their use by scientists in an attempt to prove evolution or common descent.2 What is really going on with these types of similar genes and how can they be interpreted within a special creation model as opposed to a naturalistic framework?

In very general terms, tumor suppressor genes are key genomic features (blocks of genetic code) that help regulate the growth and division of animal cells. When these genes are functioning properly, they code for proteins that can prevent or inhibit the out-of-control cell proliferation that forms the basis for the growth of tumors. When tumor suppressor genes are inactivated due to a DNA mutation, cell growth and division are no longer kept in check, resulting in cancer.

There are three main types of tumor suppressor genes. One type signals cells to slow down and stop dividing. Another type of tumor suppressor gene produces a protein that is responsible for checking and fixing damage in DNA that can happen when cells divide and proliferate. A third is responsible for telling cells when to die in a process called apoptosis. Cell growth, proliferation, and controlled cell death are essential to the development and maintenance of all animal systems.

For example, human hands develop from an initial fan-shaped structure, where apoptosis (programmed cell death) removes cells between fingers, and cell growth and division build up the fingers. How these genes are regulated will vary with the organism. However, because the basic aspects of the cell cycle are generally similar in many animals, one would actually expect a high level of DNA sequence conservation (similarity) between the coding parts of the genes as well as the proteins they produce.

The Ultimate Genetic Programmer

Generally, the more common a cellular process is between organisms, the more similar its various components will be. Does this indicate random chance evolutionary processes, or could it be an example of the Creator’s wise and efficient use and re-use of genetic code in different creatures to accomplish a common and basic cellular function?

Consider the computer world. Ask seasoned computer programmers how often they completely re-write long, complicated blocks of code when they already have what they need somewhere on file. When a long piece of previously-written code is needed and available, programmers will tailor it to fit in its new context, but they will usually not completely re-write it.

Of course, God is the ultimate programmer, and the genetic code He developed will produce the best possible protein needed for the system in which it works. If another organism has a similar physiology, one can expect many of the same genes to be present in its genome. There are a finite number of ways to accomplish the same task in cells. Thus, the genes that are used to accomplish that task will usually be quite similar, with minor key variations. These slight differences exist because the Creator has optimized the genes for that particular kind of creature and its biochemistry.

What the data really show is that high levels of efficiency and utility in genetic information seem to be a recurring theme in the study of genomes. In fact, with the limited number of genes in the human genome (about 25,000), over one million different protein variants are derived.3 Although not the topic of this article, a single animal gene can code for a wide variety of different proteins through a variety of complicated regulatory mechanisms. When scientists discovered this phenomenon, it totally negated the one-gene/one-protein mentality that originally existed when DNA sequence first began to be studied. That is pretty efficient code usage, which has never been equaled by even the most complex computer programs devised by man.

Genetic Regulatory Elements


While evolutionists have focused on genes that code for proteins, work is just beginning on an equally essential and complicated class of DNA sequence called regulatory elements. These are DNA sequences that do not code for protein but are involved in the regulation of genes. While efficient code usage and re-usage is common among many genomes, what is important is not just the protein the gene generates, but how much, how often, how fast, and when and where in the body it is produced. This is where the gene regulatory process begins to get really complicated. These regulatory differences play a key role in defining what makes a certain kind of organism unique.

After the human genome sequence was obtained to a completion level satisfactory to the scientific community, a separate but heavily-funded and related effort was initiated called the ENCODE (ENCyclopedia of DNA Elements) project.4 This involves ongoing research to determine the identity and characteristics of the regulatory elements in the human genome. At present, ENCODE has barely scratched the surface, but the results have revolutionized the concept of genetics by showing whole new levels of complexity and efficiency of code and gene activation.

Conclusion


The genetic picture that is beginning to emerge is one of incredible networked and regulatory complexity combined with an extremely high level of efficiency in code usage--certainly nothing that could have evolved on its own through chance random evolutionary processes. As is easily seen, trying to use common genes related to common processes as proof of evolution quickly falls apart in light of the bigger genomic picture. In fact, it really speaks of smart coding by the ultimate bio-systems programmer--God Himself.

The are fundamental differences between archaeal and bacterial–eukaryotic phospholipids and, more specifically, the apparently unrelated nature of the pathways that synthesize the two opposed glycerol phosphate stereoisomers 13 The asymmetry of the glycerol phosphate stereoisomers — G1P in archaea and G3P in bacteria and eukaryotes —that are synthesized by non-homologous glycerol phosphate dehydrogenases  is the only inviolate difference.

If its inviolable, it means the membranes had to emerge separately.

1) http://www.evolutionnews.org/2007/04/francix_x_clines_an_excellent003528.html
2) http://www.ncbi.nlm.nih.gov/pubmed/19716618
3) http://www.truthinscience.org.uk/tis2/index.php/component/content/article/143.html
4) http://www.icr.org/article/common-dna-sequences-evidence-evolution/
5) http://www.somosbacteriasyvirus.com/rooting.pdf
6) http://www.biologydirect.com/content/6/1/36
7) http://www.pnas.org/content/104/7/2043.full.pdf
8 )http://mmbr.asm.org/content/75/3/423.full.pdf
9) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC135240/
10) W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree,” Science 284 (1999): 2124–28. W. Ford Doolittle, “Lateral Genomics,” Trends in Biochemical Sciences 24 (1999): M5– M8. W. Ford Doolittle, “Uprooting the Tree of Life,” Scientific American 282 (February, 2000): 90– 95.
11) Carl Woese, “On the evolution of cells,” Proceedings of the National Academy of Sciences USA 99 (2002): 8742–47. Carl R. Woese, “A New Biology for a New Century,” Microbiology and Molecular Biology Reviews 68 (2004): 173–86. Eric Bapteste, Yan Boucher, Jessica Leigh, and W. Ford Doolittle, “Phylogenetic Reconstruction and Lateral Gene Transfer,” Trends in Microbiology 12 (2004), 406–11. E. Bapteste, E. Susko, J. Leigh, D. MacLeod, R. L. Charlebois, and W. F. Doolittle, “Do Orthologous Gene Phylogenies Really Support Tree-Thinking?” Biomed Central Evolutionary Biology 5 (2005), 33. Available online (June 2006) at: http://www.biomedcentral.com/content/pdf/1471-2148-5-33.pdf. S. L. Baldauf, “The Deep Roots of Eukaryotes,” Science 300 (2003), 1703–06.
12) http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005912
13) http://fire.biol.wwu.edu/cmoyer/zztemp_fire/biol345_F13/papers/Lombard_membranes_3domains_natrevmicro12.pdf
14) http://www.sciencedirect.com/science/article/pii/S0958166914002353
15) http://jeb.biologists.org/content/206/17/2911
16. Intracellular Calcium, page 577
17. ORIGIN, EVOLUTION, EXTINCTION,  THE EPIC STORY OF LIFE ON EARTH, page 10

More readings:

Common descent
http://reasonandscience.heavenforum.org/t1615-common-descent

http://sciencerefutesevolution.blogspot.com.br/2017/06/a-comparison-of-two-models-of-origin-of.html



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Human-Chimp Similarities: Common Ancestry or Flawed Research? 1

In 2003, the human genome was heralded as a near-complete DNA sequence, except for the repetitive regions that could not be resolved due to the limitations of the prevailing DNA sequencing technologies.1 The chimpanzee genome was subsequently finished in 2005 with the hope that its completion would provide clear-cut DNA similarity evidence for an ape-human common ancestry.2 This similarity is frequently cited as proof of man's evolutionary origins, but a more objective explanation tells a different story, one that is more complex than evolutionary scientists seem willing to admit.

Genomics and the DNA Revolution

One of the main problems with a comparative evolutionary analysis between human and chimp DNA is that some of the most critical DNA sequence is often omitted from the scope of the analysis. Another problem is that only similar DNA sequences are selected for analysis. As a result, estimates of similarity become biased towards the high side. An inflated level of overall DNA sequence similarity between humans and chimps is then reported to the general public, which obviously supports the case for human evolution. Since most people are not equipped to investigate the details of DNA analysis, the data remains unchallenged.

The supposed fact that human DNA is 98 to 99 percent similar to chimpanzee DNA is actually misleading.

The availability of the chimp genome sequence in 2005 has provided a more realistic comparison. It should be noted that the chimp genome was sequenced to a much less stringent level than the human genome, and when completed it initially consisted of a large set of small un-oriented and random fragments. To assemble these DNA fragments into contiguous sections that represented large regions of chromosomes, the human genome was used as a guide or framework to anchor and orient the chimp sequence. Thus, the evolutionary assumption of a supposed ape to human transition was used to assemble the otherwise random chimp genome.

At this point in time, a completely unbiased whole genome comparison between chimp and human has not been done and certainly should be. Despite this fact, several studies have been performed where targeted regions of the genomes were compared and overall similarity estimates as low as 86 percent were obtained.3 Once again, keep in mind that these regions were hand-picked because they already showed similarity at some level. The fact remains that there are large blocks of sequence anomalies between chimp and human that are not directly comparable and would actually give a similarity of 0 percent in some regions. In addition, the loss and addition of large DNA sequence blocks are present in humans and gorillas, but not in chimps and vice versa. This is difficult to explain in evolutionary terms since the gorilla is lower on the primate tree than the chimp and supposedly more distant to humans. How could these large blocks of DNA--from an evolutionary perspective--appear first in gorillas, disappear in chimps, and then reappear in humans?

Analyzing the Source of Similarity

So how exactly did scientists come up with the highly-touted 98 to 99 percent similarity estimates?

First, they used only human and chimp DNA sequence fragments that already exhibited a high level of similarity. Sections that didn't line up were tossed out of the mix. Next, they only used the protein coding portions of genes for their comparison. Most of the DNA sequence across the chromosomal region encompassing a gene is not used for protein coding, but rather for gene regulation, like the instructions in a recipe that specify what to do with the raw ingredients.3 The genetic information that is functional and regulatory is stored in "non-coding regions," which are essential for the proper functioning of all cells, ensuring that the right genes are turned on or off at the right time in concert with other genes. When these regions of the gene are included in a similarity estimate between human and chimp, the values can drop markedly and will vary widely according to the types of genes being compared.

The diagram in Figure 1 illustrates how a gene is typically represented as a portion of a chromosome. As indicated, there is considerably more non-coding sequence ahead of the gene, within it ("introns"), and behind it. The 98 to 99 percent sequence similarity estimates are often derived from the small pieces of coding sequence ("exons"). Other non-coding sequences, including the introns and sequences flanking the gene region, are often omitted in a "gene for gene" comparative analysis. The critical importance of the non-coding sequences in the function of the genome was not well understood until recently, but this does not excuse the bias of the "98 to 99 percent similarity" claim.

Another important factor concerns the potential for variants of the same protein to have different functions that can perform different tasks in different tissues. There is now no doubt that gene or protein sequence similarities, in and of themselves, are not as significant as other functional and regulatory information in the cell. Unfortunately, evolutionary assumptions drove a biased approach of simple sequence comparisons, providing few answers as to why humans and chimps are obviously so different.

Interestingly, current research is confirming that most of what makes humans biologically unique when compared to chimps and other animals is how genes are controlled and regulated in the genome. Several studies within the past few years are demonstrating clear differences in individual gene and gene network expression patterns between humans and chimps in regard to a wide number of traits.4, 5 Of course, the largest differences are observed in regard to brain function, dexterity, speech, and other traits with strong cognitive components. To make the genetic landscape even more complicated, a number of recent studies are also confirming that close to 93 percent of the genome is transcriptionally active (functional).6 Not so long ago, scientists thought that only 3 to 5 percent of the genome that contained the protein coding regions was functional; the rest was considered "junk DNA."

Conclusion

So what is an appropriate response to the assertion that a 99 percent similarity exists between human and chimp DNA, and thus proves common ancestry?

One can simply say that the whole genomes have never really been compared, only hand-selected regions already known to be similar have been examined, and the data is heavily biased. In fact, due to limitations in DNA sequencing technology, researchers do not even have the complete genomic sequence for human or chimp at present. In the sequence that they do have, much more analysis needs to be done.

Here are a number of key points that counter the evolutionary claims of close human-chimp similarity:

  The chimp genome is 10 to 12 percent larger than the human genome and is not in a near-finished state like the human genome; it is considered a rough draft.

  When large regions of the two genomes are compared, critical sequence dissimilarities become evident.

  Extremely large blocks of dissimilarity exist on a number of key chromosomes, including marked structural differences between the entire male (Y) chromosomes.

  Distinct differences in gene function and regulation are now known to be a more significant factor in determining differences in traits between organisms than the gene sequence alone. Research in this area has clearly demonstrated that this is the case with humans and apes, where marked dissimilarities in expression patterns are evident.

It is clear that the only way to obtain extreme DNA-based similarity between man and chimpanzee is to use comparative analyses that are heavily skewed by an evolutionary bias where one picks and chooses what data or what part of the genome to use. At present, the DNA sequence differences between these genomes clearly indicate a much lower level than 98 to 99 percent. In fact, one evolutionary study suggests it may be as low as 86 percent or less. In addition, the complex functional aspects of genes and their regulatory networks differ markedly between humans and chimps and play a more important role than DNA sequence by itself.

The DNA data, both structural and functional, clearly supports the concept of humans and chimps created as distinct separate kinds. Not only are humans and chimps genetically distinct, but only man has the innate capacity and obligation to worship his Creator.7

Newly Discovered 'Orphan Genes' Defy Evolution 2

An important category of "rogue" genetic data that utterly defies evolutionary predictions is the common occurrence of taxonomically restricted genes, otherwise known as "orphan genes." These are now being discovered in the sequencing of all genomes.

Many multicellular animals share similar sets of genes that produce proteins that perform related biochemical functions. This is a common feature of purposefully engineered systems. In addition to these standard genes, all organisms thus far tested also have unique sets of genes specific to that type of creature.

The authors of a recent review paper, published in Trends in Genetics, on the subject of orphan genes stated, "Comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs [similar counterparts] in other species."1

These orphan genes are also being found to be particularly important for specific biological adaptations that correspond with ecological niches in relation to the creature's interaction with its environment.2 The problem for the evolutionary model of animal origins is the fact that these DNA sequences appear suddenly and fully functional without any trace of evolutionary ancestry (DNA sequence precursors in other seemingly related organisms). And several new studies in both fish and insect genomes are now highlighting this important fact.

In the recent fish study, researchers sequenced the protein-coding genes in zebrafish and then compared the DNA sequences to other animal's gene sequences.3 The researchers classified the zebrafish genes into three different groups: 1) Genes commonly found in many types of animals, 2) genes that are only found in ray-finned fishes (the broad group of Teleost fishes), and 3) genes that are species-specific to only zebrafish. This third category refers to orphan genes. Thus there was a distinct group of genes found only associated with zebrafish and no other animal or type of fish.

In another study, researchers compared the genomes of seven different types of ants with other known insect genomes.4 When comparing the ant genes to other insects, researchers discovered 28,581 genes that were unique only to ants and not found in other insects. While the various ant species shared many groups of genes, only 64 genes were common to all seven ant species.

The researchers concluded that on average, each ant species contained 1,715 unique genes—orphan genes. Researchers not only found dramatic differences for protein-coding genes, but also for other types of regulatory DNA sequences that control how and when genes are turned off and on.

While these results clearly defy evolution, what do they mean within a biblical creation framework of origins? In the book of Genesis, created kinds of organism are defined as being able to reproduce and interbreed “after their kind.” These different ant species are not inter-fertile and they also inhabit different ecological niches, utilize different types of food sources, and have different types of social structures important to communal insects such as ants and bees. Combined with the fact that they also have unique gene sets, they possibly all descended from different created ant kinds.

While these orphan genes challenge evolution, they help creationists understand the patterns of genetic diversity related to created kinds. And ants may be a good example of animals that did not need to be saved from the Genesis flood by being sequestered on the ark, since they might have survived outside, on floating mats of vegetation. Ants would have, to some extent, also avoided a severe genetic bottleneck.5 If so, their present diversity would more closely represent the originally created array of ant genomes.

Clearly, the complexity and design of God's creation is astounding, vast, and incredibly amazing. Only an Omnipotent and Wise Creator could have been the source of these widely diverse, and yet complicated and precise genetic arrangements.


Cells' Molecular Motor Diversity Confounds Evolution 6

Scientists believe that the study of genes that encode the proteins for molecular motors will help solve the mysteries of evolution. However, the result of a study published in the journal Genome Biology and Evolution has only served to support the predictions of special creation—that unique variants of cellular complexity and innovation exist at all levels of life.1
Molecular motors are important features of eukaryotic cells that are formed by a variety of protein types. One group of molecular motors is called the myosins, which have recently been studied in everything from one-celled eukaryotes to humans. The goal of this and many other studies has been the ever-elusive characterization of the mythical Last Eukaryotic Common Ancestor (LECA).2
The fictional LECA creature represents the final stage of a transition between a bacterial-archaeal prokaryote (the smallest and simplest organism) and a one-celled eukaryote (a cell with a nucleus and other organelles). The main problem with this idea is that, not only does no such creature exist, but eukaryotes also contain molecular similarities to both bacteria and archaea—prokaryotes that are found in completely separate domains of cellular life. Another major problem is that many complex molecular and cellular features unique among eukaryotes are not found in any prokaryotes. Because of this elaborate mosaic of cellular features, the development of any evolutionary story for the origin of eukaryotes has been fraught with much difficulty.
Researchers had hoped to find that matters would be clarified by myosin proteins derived from the DNA sequences of different single-celled eukaryotes, such as flagellated protozoa (protozoa with a whip-like tail), amoeboid protozoa, and algae.1 Instead of finding a pattern of evolving myosin "motor" genes (simple to complex) as life seemingly became more advanced, they found that the highest numbers of different types of myosin genes were found in single-celled eukaryotes. The authors stated, "The number of myosin genes varies markedly between lineages [types of eukaryotes]," and "holozoan genomes, as well as some amoebozoans and heterokonts, have the highest numbers of myosins of all eukaryotes. In particular, the haptophyte Emiliania huxleyi has the highest number of myosin genes (53), followed by the ichthyosporean Pirum gemmata (43), the filasterean M. vibrans (39), and the metazoan Homo sapiens(38)."1
The end result of all this labor was ultimately counterproductive to the formation of any sort of evolutionary tree. The researchers stated, "We do not aim to infer a eukaryotic tree of life from the myosin genomic content."1 This is because the data was not amenable to do so. Instead, they noted that "we provide an integrative and robust classification, useful for future genomic and functional studies on this crucial eukaryotic gene family."1
So, how did the authors explain the incredible complexity found across the spectrum of life in myosin gene content that had no clear evolutionary patterns? They explained it by 1) convergence (the sudden and simultaneous appearance of a gene with no evolutionary patterns in different taxa), 2) lineage-specific expansions (different myosin gene complements found in different creatures), and 3) gene losses (missing genes that evolutionists thought should have been there). None of these ideas actually explain why there is no evolutionary pattern of simple-to-complex in myosin gene content across the spectrum of life. Specifically, the ideas of convergent evolution and lineage-specific expansions are nothing more than fancy terms for the fact that these different types of myosin genes appeared suddenly in unrelated creatures at the same time.
Clearly, the only scientific model that predicts this type of molecular and cellular complexity and innovation across all forms of life is one associated with special creation. Each created kind is genetically unique and has its own special and complex gene repertoire needed for the niche that it fills.


Chinese Researchers Demolish Evolutionary Pseudo-Science 3


In recent decades the genomes of several species have been mapped out and evolutionists are using these genome data to refine their theory. They are also making some high claims. The genome data sets, say evolutionists, are adding striking new confirmations for their theory. One piece of evidence evolutionists point to is the high similarity between the human and chimpanzee genomes. The two genomes are about 95% the same and evolutionists say this shows how easily the human could have evolved from a chimp-human common ancestor. Evolution professor Dennis Venema explains

For example, humans and our closest relatives, chimpanzees, have genomes that are around 95% identical, and most of the DNA differences are not differences that actually affect our forms. So, small changes accruing over time since we last shared a common ancestor was enough to shape our species since we parted ways – there is no evidence that evolution requires radical changes at the DNA level.

No evidence? This is an example of evolutionists seeing what they want to see in the data. Evolutionists are driven by their metaphysics and so want to believe that we are descended from a primitive ape creature. They want to believe that humans and apes “are one” and that the wall between human and animal “has been breached,” as the Smithsonian Institute put it.

But as I pointed out in my book Darwin’s Proof, if the DNA comparisons between human and chimp don’t reveal much significant difference, then we probably need to look elsewhere. Humans are vastly different than chimps and if our DNA comparisons aren’t revealing much difference, then those segments probably aren’t what is driving the difference between the two species.

In fact there are much more significant differences between the human and chimp genomes. Differences that may “actually affect our forms.” A 2011 paper out of China and Canada, for example, found 60 protein-coding genes in humans that are not in the chimp. And that was an extremely conservative estimate. They actually found evidence for far more such genes, but used conservative filters to arrive at 60 unique genes. Not surprisingly, the research also found evidence of function, for these genes, that may be unique to humans.

If the proteins encoded by these genes are anything like most proteins, then this finding would be another major problem for evolutionary theory. Aside from rebuking the evolutionist’s view that the human-chimp genome differences must be minor, 6 million years simply would not be enough time to evolve these genes.

In fact, 6 billion years would not be enough time. The evolution of a single new protein, even by evolutionists’ incredibly optimistic assumptions, is astronomically unlikely, even given the entire age of the universe to work on the problem.

Unfortunately none of this will influence the evolutionist because for evolutionists this never was about science. As Venema explains:

It’s one thing to explain away biogeographical patterns or claim that anatomical similarities reflect a non-evolutionary “design” pattern – but another thing altogether to attempt to explain away why humans (and other placental mammals) have a defective gene for making egg yolk in the exact spot in our genomes where chickens have the functional version of this gene, and that humans and chimpanzees share a large number of mutations in common in our two inactivated copies.


The argument from dysteleology says that these faulty genetics would not have been designed or created and that therefore they must have evolved. This argument is not new. It did not arise when the genomic data became available but has been influential for centuries. Earlier evolutionists found faults with all manner of biological, geological and cosmological aspects of nature.

This reasoning is not new and it is not science. It is based on personal religious beliefs that are not open to debate. Imagine if you believed these things. Imagine that you believed, with Venema, that common mutations, for example, rules out any possibility of the species having been created in any sort of direct sense.

Then of course you would be an evolutionist. Even though evolutionary theory fails every test. With evolution, the religion drives the science.

In the meantime, while the evolutionists make up rules for science to follow and insist the world spontaneously arose in spite of the evidence, these researchers in China and Canada are doing real science.

A Primer on the Tree of Life 4

Evolutionists often claim that universal common ancestry and the “tree of life” are established facts. One recent opinion article in argued, “The evidence that all life, plants and animals, humans and fruit flies, evolved from a common ancestor by mutation and natural selection is beyond theory. It is a fact. Anyone who takes the time to read the evidence with an open mind will join scientists and the well-educated.”1 The take-home message is that if you doubt Darwin’s tree of life, you’re ignorant. No one wants to be ridiculed, so it’s a lot easier to buy the rhetoric and “join scientists and the well-educated.” 


But what is the evidence for their claim, and how much of it is based upon assumptions? The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified. 


Some of these ad hoc rationalizations may appear reasonable — horizontal gene transfer, convergent evolution, differing rates of evolution (rapid evolution is conveniently said to muddy any phylogenetic signal), fusion of genomes — but at the end of the day, we must call them what they are: ad hoc rationalizations designed to save a theory that has already been falsified. Because it is taken as an assumption, evolutionists effectively treat common ancestry in an unfalsifiable and unscientific fashion, where any data that contradicts the expectations of common descent is simply explained away via one of the abovead hoc rationalizations. But if we treat common descent as it ought to be treated — as a testable hypothesis — then it contradicts much data. 


The Main Assumption
As noted, the first assumption that goes into tree-building is the basic assumption that similarity between different organisms is the result of inheritance from a common ancestor. That is, except for when it isn’t. (And then the similarity is purportedly said to be the result of convergent evolution, etc.) But even if we take this claim at face value — that similarity between different organisms is the result of inheritance from a common ancestor — let’s recognize it for what it is: a mere assumption. But are there other possibilities? 


The Molecular Evidence
When speaking to the public, evolutionists are infamous for overstating the evidence for universal common ancestry. For example, when speaking before the Texas State Board of Education in January, 2009, University of Texas evolutionist biologist David Hillis cited himself as one of the “world’s leading experts on the tree of life” and later told the Board that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. But this is not accurate. Indeed, in the technical scientific literature, one finds a vast swath of scientific papers that have found contradictions, inconsistencies, and flat out failures of the molecular data to provide a clear picture of phylogenetic history and common descent. 


Indeed, the cover story of the journal New Scientist, published on the very day that Dr. Hillis testified, was titled, “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’ gross oversimplification of molecular systematics, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:“For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.2Of course, these scientists are all committed evolutionists, which makes their admissions all the more weighty. To reiterate, the basic problem is that one gene or protein yields one version of the “tree of life,” while another gene or protein yields an entirely different tree. As the New Scientist article stated:The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.3Likewise, leading evolutionary bioinformatics specialist W. Ford Doolittle explains, “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.”4 Hillis (and others) may claim that this problem is only encountered when one tries to reconstruct the evolutionary relationships of microorganisms, such as bacteria, which can swap genes through a process called “horizontal gene transfer,” thereby muddying any phylogenetic signal. But this objection doesn’t hold water because the tree of life is challenged even among higher organisms where such gene-swapping does not take place. As the article explains:Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts—also known as tunicates—are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says.5Even among higher organisms, “[t]he problem was that different genes told contradictory evolutionary stories,” leading Syvanen to say, regarding the relationships of these higher groups, “We’ve just annihilated the tree of life.” This directly contradicts Hillis’ claim that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence.” 


Other scientists agree with the conclusions of the New Scientist article. Looking higher up the tree, a recent study published in Science tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.”6 Likewise, Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seeneverywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”7 


Likewise, National Academy of Sciences biologist Lynn Margulis has had harsh words for the field of molecular systematics, which Hillis studies. In her article, “The Phylogenetic Tree Topples,” she explains that “many biologists claim they know for sure that random mutation (purposeless chance) is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk, dichotomously branching-phylogenetic-tree pattern!” But she dissents from that view and attacks the dogmatism of evolutionary systematists, noting, “Especially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don’t study ancestors.”8 


Striking admissions of troubles in reconstructing the “tree of life” also came from a paper in the journal PLOS Biology entitled, “Bushes in the Tree of Life.” The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.”9 The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.”10 The paper even contends that “[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”11 


Unfortunately, one assumption that these evolutionary biologists aren’t willing to consider changing is the assumption that neo-Darwinism and universal common ancestry are correct. 


Extreme Genetic Convergent Similarity: Common Design or Common Descent?
If common descent is leading to so many bad predictions, why not consider the possibility that biological similarity is instead the result of common design? After all, designers regularly re-use parts, programs, or components that work in different designs (such as using wheels on both cars and airplanes, or keyboards on both computers and cell-phones). 


One data-point that might suggest common design rather than common descent is the gene “pax-6.” Pax-6 is one of those pesky instances where extreme genetic similarity popped up in a place totally unexpected and unpredicted by evolutionary biology. In short, scientists have discovered that organisms as diverse as jellyfish, arthropods, mollusks, and vertebrates all use pax-6 to control development of their very distinct types of eyes. Because their eye-types are so different, it previously hadn’t been thought that these organisms even shared a common ancestor with an eye. Evolutionary biologist Ernst Mayr explains the havoc wreaked within the standard evolutionary phylogeny when it was discovered that the same gene controlled eye-development in many organisms with very different types of eyes:It had been shown that by morphological-phylogenetic research that photoreceptor organs (eyes) had developed at least 40 times independently during the evolution of animal diversity. A developmental geneticist, however, showed that all animals with eyes have the same regulator gene, Pax 6, which organizes the construction of the eye. It was therefore concluded at first concluded that all eyes were derived from a single ancestral eye with the Pax 6 gene. But then the geneticist also found Pax 6 in species without eyes, and proposed that they must have descended from ancestors with eyes. However, this scenario turned out to be quite improbable and the wide distribution of Pax 6 required a different explanation. It is now believed that Pax 6, even before the origin of eyes, had an unknown function in eyeless organisms, and was subsequently recruited for its role as an eye organizer.12Typically, extreme genetic similarity is thought to mandate inheritance from a common ancestor, because the odds of different species independently arriving at the same genetic solution are exceedingly small. But if we require a Darwinian evolutionary scheme, such an improbable event is exactly what must have occurred. The observed distribution of genes like pax-6 demand extreme “convergent evolution” at the genetic level. Mayr tries to argue that such improbable examples of extreme genetic convergent evolution are not not only acceptable, but common: That a structure like the eye could originate numerous times independently in very different kinds of organisms is not unique in the living world. After photoreceptors had evolved in animals, bioluminescence originated at least 30 times independently among various kinds of organisms. In most cases, essentially similar biochemical mechanisms were used. Virtually scores of similar cases have been discovered in recent years, and they often make use of hidden potentials of the genotype inherited from early ancestors.13Mayr tries to explain away this extreme genetic convergent similarity by appealing to “hidden potentials of the genotype.” Does this sound compatible with the kind of blind, unguided, and even random processes inherent in neo-Darwinian evolution? No. This sounds like a goal-directed process — intelligent design. 


Homology in Crisis
As Mayr suggests, there are other examples where genetic similarity appears in unexpected places. Biologically functional similarity that is thought to be the result of inheritance from a common ancestor is called “homology.” 


The concept of “homology” has been thrown into a crisis via observations, like those of Mayr, that the same genes control the growth of non-homologous body parts. Pax-6 is just one example. Another is the fact that the same gene controls the development of limbs in widely diverse types organisms that have wholly different types of limbs, where their common ancestor is not thought to have a common type of limb.14 The methodology used to infer homology was also challenged when it was discovered that different developmental pathways control the growth of body parts otherwise thought to be homologous. As the textbook Explore Evolution observes:In sharks, for example, the gut develops from cells in the roof of the embryonic cavity. In lampreys, the gut develops from cells on the floor of the cavity. And in frogs, the gut develops from cells from both the roof and the floor of the embryonic cavity. This discovery—that homologous structures can be produced by different developmental pathways—contradicts what we would expect to find if all vertebrates share a common ancestor. … To summarize, biologists have made two discoveries that challenge the argument from anatomical homology. The first is that the development of homologous structures can be governed by different genes and can follow different developmental pathways. The second discovery, conversely, is that sometimes the same gene plays a role in producing different adult structures. Both of these discoveries seem to contradict neo-Darwinian expectations.15Perhaps this evidence is just the result of what Mayr called “hidden potentials of the genotype,” or perhaps it contradicts neo-Darwinian expectations because neo-Darwinism is wrong. 


Molecules Contradict Morphology
A final way that evolutionists overstate the evidence for common descent is by claiming that molecular phylogenies have confirmed or buttressed phylogenies based upon morphology. For example, in his book Galileo’s Finger, Oxford University scientist Peter Atkins discusses evolution and boldly states, “The effective prediction is that the details of molecular evolution must be consistent with those of macroscopic evolution.”16 Likewise, when testifying before the Texas State Board of Education, David Hillis claimed that “there’s overwhelming correspondence between the basic structures we have about the tree of life from anatomical data, from biochemical data, molecular sequence data.” Yet a variety of studies — typically unmentioned when evolutionists promote common descent to the public — have recognized that evolutionary trees based upon morphology (physical characteristics of organisms) or fossils, commonly conflict with evolutionary trees based upon DNA or protein sequences (also called molecule-based trees). 


One authoritative review paper by Darwinian leaders in this field stated, “As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology.”17 Another set of pro-evolution experts wrote, “That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent."18 


For example, pro-evolution textbooks often tout the Cytochrome C phylogenetic tree as allegedly matching and confirming the traditional phylogeny of many animal groups. This is said to bolster the case for common descent. However, evolutionists cherry pick this example and rarely talk about the Cytochrome B tree, which has striking differences from the classical animal phylogeny. As one article in Trends in Ecology and Evolution stated: “the mitochondrial cytochrome b gene implied...an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.”19 


The widespread prevalence of disagreement and non-correspondence between molecule-based evolutionary trees and anatomy-based evolutionary trees led to a major article in Nature that reported that “disparities between molecular and morphological trees” lead to “evolution wars” because “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”20 The article’s revelation of the disparities between molecular and morphological phylogenies was striking:When biologists talk of the ‘evolution wars’, they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species' morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history. … So can the disparities between molecular and morphological trees ever be resolved? Some proponents of the molecular approach claim there is no need. The solution, they say, is to throw out morphology, and accept their version of the truth. “Our method provides the final conclusion about phylogeny,” claims Okada. Shared ancestry means a genetic relationship, the molecular camp argues, so it must be better to analyse DNA and the proteins it encodes, rather than morphological characters that can end up looking similar as a result of convergent evolution in unrelated groups, rather than through common descent. But morphologists respond that convergence can also happen at the molecular level, and note there is a long history of systematists making large claims based on one new form of evidence, only to be proved wrong at a later date.21Likewise, a review article in the journal Bioessays reported that despite a vast increase in the amount of data since Darwin’s time, “our ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years,” and that, “[d]espite increasing methodological sophistication, phylogenies derived from morphology, and those inferred from molecules, are not always converging on a consensus.”22 Strikingly, an article in Trends in Ecology and Evolutionconcluded, “the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows.”23 


Despite the inaccurate claims of some evolutionists and their cherry picking of data, the truth is that there is great incongruence between these two different types of phylogenies, and that this incongruence is a huge issue, problem, and debate within systematics. 


Conclusion
The methodology for inferring common descent has broken down. Proponents of neo-Darwinian evolution are forced into reasoning that similarity implies common ancestry, except for when it doesn’t. And when it doesn’t, they appeal to all sorts of ad hoc rationalizations to save common ancestry. Tellingly, the one assumption and view that they are not willing to jettison is the overall assumption of common ancestry itself. This shows that evolutionists treat common descent in an unfalsifiable, and therefore unscientific and ideological, fashion. 


Meanwhile, as far as the data is concerned, the New Scientist article admits, “Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth,” but because “different genes told contradictory evolutionary stories,” the notion of a tree of life is now quickly becoming a vision of the past — as the article stated, it’s being “annihilated.” Perhaps the reason why different genes are telling “different evolutionary stories” is because the genes have wholly different stories to tell, namely stories that indicate that all organisms are not genetically related. For those open-minded enough to consider it, common design is a viable alternative to common descent. 

Summary of Breakdowns in Attempts to Reconstruct the Tree of Life 5

When arguing for common descent, evolutionary scientists typically assert that the degree of genetic (or anatomical) similarity between two species indicates how closely they are related. But there are numerous cases where this assumption fails, and anatomical or molecular data yield evolutionary trees (called ‘phylogenies’) that conflict with conventional views of organismal relationships. The basic problem is that evolutionary trees based on one gene commonly differ strikingly from a phylogeny based on a different gene.

Leading evolutionists are loath to admit this fact during public debate. During the 2009 Texas State Board of Education (TSBOE) hearings on evolution-education, University of Texas Austin evolutionary scientist David Hillis cited himself as a “world’s leading exper[t] on the tree of life” and told the TSBOE that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. Hillis’s self-proclaimed expertise makes it all the more disconcerting that he tried to mislead the TSBOE about the widespread prevalence of incongruencies between various molecular phylogenies within his own field.

Indeed, the very day that Hillis testified before the TSBOE, the journal New Scientist published a cover story titled “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’s gross oversimplification of the case for common ancestry, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart: “For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.1 To reiterate, the basic problem is that one gene or protein yields one version of the “tree of life,” while another gene or protein yields an entirely different tree. As the New Scientist article stated: The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.2 Likewise, leading evolutionary bioinformatics specialist W. Ford Doolittle explains, “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.”3 Evolutionary biologists like Doolittle may claim that this problem is encountered when one tries to reconstruct the evolutionary relationships of microorganisms, such as bacteria, which can swap genes through a process called horizontal gene transfer, thereby muddying any phylogenetic signal. But this objection does not hold water, since the tree of life is challenged even among higher organisms where such gene-swapping is not observed. As the New Scientist article noted, “research suggests that the evolution of animals and plants isn't exactly tree-like either.”

Authority Carl Woese has also observed that these problems extend well beyond the base of the tree of life, stating: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”4 To reiterate, even among higher organisms, as the New Scientist article explains that “The problem was that different genes told contradictory evolutionary stories,” therefore leading one scientist to say regarding the relationships of these higher groups, “We’ve just annihilated the tree of life.” Many studies have reported such problems:
A 2009 paper in Trends in Ecology and Evolution notes that: “A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome.”5 Similarly, a paper in the journal Genome Research studied the DNA sequences in various animal groups and found that “different proteins generate different phylogenetic tree[s].”6
A study published in Science in 2005 tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” Again, the problem lies in the fact that trees based upon one gene or protein often conflict with trees based upon other genes. Their study tried to avoid this problem by using a many-gene technique, yet still found that “[a] 50-gene data matrix does not resolve relationships among most metazoan phyla.”7
Striking admissions of troubles in reconstructing the “tree of life” also came from a 2006 paper in the journal PLoS Biology, entitled “Bushes in the Tree of Life.” The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.” The paper even contends that “[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”8 Unfortunately one assumption they were not willing to re-evaluate is that of universal common ancestry.
Another study published in Science found that the molecular data implied that six-legged arthropods, or hexapods (i.e. insects) are not monophyletic, a conclusion that differed strikingly from virtually all previous wisdom. The article concluded “Although this tree shows many interesting outcomes, it also contains some evidently untenable relationships, which nevertheless have strong statistical support.”9
A paper in the Journal of Molecular Evolution found that molecule-based phylogenies conflicted sharply with previously established phylogenies of major mammal groups, concluding that this anomalous tree “is not due to a stochastic error, but is due to convergent or parallel evolution.”10 Likewise, a study published in Proceedings of the National Academy of Sciences USA explains that when evolutionary biologists tried to construct a phylogenetic tree for the major groups of birds using mitochondrial DNA (mtDNA), their results conflicted sharply with traditional notions of bird relationships. Strikingly, they even find “convergent” similarity between some bird mtDNA and the mtDNA of distant species such as snakes and lizards. The article suggests bird mtDNA underwent “multiple independent originations,” with their study making a “finding of multiple independent origins for a particular mtDNA gene order among diverse birds.”11
When testifying before the TSBOE, professor Hillis also made the inaccurate claim that “there’s overwhelming correspondence between the basic structures we have about the tree of life from anatomical data, from biochemical data, molecular sequence data.” Yet many evolutionary scientists have recognized that evolutionary trees based upon morphology (physical characteristics of organisms) or fossils, commonly conflict with evolutionary trees based upon DNA or protein sequences (also called molecule-based trees).

For example, a review paper by Darwinian leaders in this field stated, “As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology.”12 Another set of pro-evolution experts wrote, “That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent.”13

The widespread prevalence of disagreement and non-correspondence between molecule-based evolutionary trees and anatomy-based evolutionary trees led a review article in Nature to report that “disparities between molecular and morphological trees” cause “evolution wars” because “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”14

As one specific example, textbooks often cite the phylogenetic tree based upon cytochrome c as purportedly matching and confirming the standard anatomy-based phylogenetic tree of many vertebrates. But one paper in Trends in Ecology and Evolution noted that the cytochrome b tree yielded “an absurd phylogeny of mammals, regardless of the method of tree construction” where “[c]ats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers.” The paper concluded that “Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.”15

This problem also exists among higher primates as molecular data often conflicts with the prevalent phylogenetic tree which claims humans are most closely related to chimpanzees.16 As one article in the journal Molecular Biology and Evolution found, “[f]or about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee.”17

The common textbook claim that a universal “tree of life” has been established by congruent molecular and morphological phylogenetic trees is contradicted by much data and scientific opinion – but this information is almost always omitted from textbook instruction given to students.



1) http://www.icr.org/article/human-chimp-similarities-common-ancestry/
2) http://www.icr.org/article/newly-discovered-orphan-genes-defy/
3) http://darwins-god.blogspot.com.br/2014/01/chinese-researchers-demolish.html
4) http://www.ideacenter.org/contentmgr/showdetails.php/id/1481
5) http://www.ideacenter.org/contentmgr/showdetails.php/id/1512



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Are Rotifers Gene Stealers or Uniquely Engineered? 1

The tools of DNA sequencing are becoming cheaper to use and more productive than ever, and the deluge of DNA comparison results between organisms coming forth are becoming a quagmire for the evolutionary paradigm. To prop it up, biologists resort to ever more absurd explanations for discrepancies. A prime example of this trickery is in a recent DNA sequencing project performed in a microscopic aquatic multi-cellular animal called a rotifer.1
In this effort, the researchers targeted those gene sequences that are expressed as proteins for DNA sequencing because the genome was too large and complex to sequence and assemble all of its DNA. They recorded over 61,000 gene sequences that were expressed from rotifers grown in stressed and non-stressed conditions. Of these, they could only find sequence similarities between rotifers and other creatures for 28,922 sequences (less than half). The researchers tossed the unknown DNA sequences out of their analysis since the non-similar genes were novel, apparently specific to rotifer, and essentially difficult for evolution to explain.
Of the 28,922 sequences for which they could obtain a match in a public database of other creature's DNA and protein sequences, a significant proportion (more than in any other creature sequenced) did not fit evolutionary expectations of common descent. Further complicating this picture, the rotifer gene sequences were found in a diverse number of non-rotifer creatures! Some of the creatures that had gene matches to rotifers included a variety of plants, other multicellular animals, protists (complex single celled animals), archaea, bacteria, and fungi. Evolutionists have two options in which to categorize these unusual gene matches based on their naturalistic presuppositions. First, they can say that these genes evolved independently in separate creatures in a hypothetical process called "convergent evolution." However, in cases where there are literally hundreds of these DNA sequences popping up in multiple organisms, this scenario becomes so unlikely that even evolutionists have too much difficulty imagining it. The second option is called "horizontal gene transfer," or HGT. This involves the transfer of genes, perhaps via some sort of microbial host vector such as a bacterium.2
In the present report, the rotifer under study was asexual, limiting heredity as an option for aiding in gene transfer. So the researchers concluded that it stolehundreds of genes via HGT from a plethora of other creatures. HGT is considered somewhat common among bacteria because they form connective tubes (called pili) and exchange little bits of DNA, like sharing software. Also, HGT can occur rarely between a bacterium and a multicellular host that it interacts with during its life cycle.3
How will rotifer researchers account for the massive transfer of hundreds of genes from a broad range of hosts that they believe includes 533 supposed source genomes for which no biological host-based relationships exists? Some sort of causal host relationship must occur for the transfer of one gene, let alonehundreds of genes from hundreds of sources.1
Another problem is that the researchers showed that the so-called "stolen genes" were well-integrated into the rotifer cell biochemistry and its environmental adaptation mechanisms. A separate 2012 study showed that highly expressed native genes could not be shared via HGT, even among bacteria, because they would severely disrupt essential cell biochemistry.4 And these are exactly the types of genes that were surveyed in the rotifer.
In this case, evolutionary biologists have resorted to fictional stories cloaked in technical terminology to escape the straightforward conclusion that rotifer DNA was purposefully crafted. If a large bunch of newly discovered genes don't make evolutionary sense, then evolution proponents ascribe their origin to HGT despite the fact that HGT is not known to operate without any host-based relationship. HGT is also not known to occur en masse, and HGT of essential genes is in theory impossible.4
The unique mix of rotifer genes along with their flawless biochemical integration into the rotifer's cell system, clearly and abundantly supports the special creation described in the Bible.

Saving the Tree of Life 2

PBS asserts that "shared amino acids" in genes common to many types of organisms indicate that all life shares a common ancestor. Intelligent design is not necessarily incompatible with common ancestry, but it must be noted that intelligent agents commonly re-use parts that work in different designs. Thus, similarities in such genetic sequences may also be generated as a result of functional requirements and common design rather than by common descent.

In fact, PBS's statement is highly misleading. Darwin's tree of life--the notion that all living organisms share a universal common ancestor--has faced increasing difficulties in the past few decades. Phylogenetic trees based upon one fundamental gene or protein often conflict with trees based upon another gene or protein. In fact, this problem is particularly acute when one studies the "ancient" genes at the base of the tree of life, which PBS wrongly claims demonstrate universal common ancestry. As W. Ford Doolittle explains, "[m]olecular phylogenists will have failed to find the 'true tree,' not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree."1

Doolittle, a Darwinian biologist, elsewhere writes that "there would never have been a single cell that could be called the last universal common ancestor."2 Doolittle attributes his observations to gene-swapping among microorganisms at the base of the tree. But Carl Woese, the father of evolutionary molecular systematics, finds that such problems exist beyond the base of the tree: "Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves."3

Looking higher up the tree, a recent study conducted by Darwinian scientists tried to construct a phylogeny of animal relationships but concluded that "[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved."4 The basic problem is that phylogenetic trees based upon one gene or other characteristic will commonly conflict with trees based upon another gene or macro-characteristic. Indeed, the Cambrian explosion, where nearly all of the major living animal phyla (or basic body plans) appeared over 500 million years ago in a geological instant, raises a serious challenge to Darwinian explanations of common descent.

The nice, neat, nested hierarchy of a grand Tree of Life predicted by Darwinian theory has not been found. Evolutionary biologists are increasingly appealing to epicycles like horizontal gene transfer, differing rates of evolution, abrupt molecular radiation, convergent evolution (even convergent molecular evolution), and other ad hoc rationalizations to reconcile discrepancies between phylogenetic hypothesis. Darwinian biology is not explaining the molecular data; it is forced to explain away the data. PBS paints a rosy picture of the data, when the data isn't good news for Darwinism.

Strange Findings on Comb Jellies Uproot Animal Family Tree 3

Complete sequence of comb jelly genome reveals a separate course of evolution.



The new study on ctenophores, such as the American comb jelly above, "really shakes up how we think animal complexity evolved."

PHOTOGRAPH BY GEORGE GRALL, NATIONAL GEOGRAPHIC CREATIVE


A close look at the nervous system of the gorgeously iridescent animal known asthe comb jelly has led a team of scientists to propose a new evolutionary history: one for the comb jelly, and one for everybody else.
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"It's a paradox," said Leonid Moroz, a neurobiologist at the University of Florida in Gainesville and lead author of a paper in today's Nature about the biology of the comb jelly nervous system. "These are animals with a complex nervous system, but they basically use a completely different chemical language" from every other animal. "You have to explain it one way or another."
The way Moroz explains it is with an evolutionary scenario—one that's at odds with traditional accounts of animal evolution.
Moroz and his colleagues have been studying comb jellies, whose scientific name is ctenophores (pronounced TEN-o-fors), for many years, beginning with the sequencing of the genome of one species, the Pacific sea gooseberry, in 2007. The sea gooseberry has 19,523 genes, about the same number as are found in the human genome.
The scientists enlarged their library to the genes of ten other species of comb jelly (out of the 150 or so species known to exist) and compared them to the analogous genes in other animals. And when they looked at the genes involved in the nervous system, they found that many considered essential for the development and function of neurons were simply missing in the comb jelly.
Some of those missing genes are involved in building neurons in embryos. The cells in any animal start out in the embryo as stem cells, looking pretty much identical to one another and capable of turning into any particular type of cell. Only later in embryonic development do some stem cells switch on specific genes that transform them into neurons. This process is much the same in humans as it is in flies, slugs, and just about every other animal with a nervous system.
But comb jellies, Moroz and his colleagues found, lack those neuron-building genes altogether. Which means that comb jelly embryos must build their neurons from a different set of instructions—instructions no one yet understands.
Nor do comb jellies use the standard complement of neurotransmitters found in other animals, the scientists found. The genes for most of the neurotransmitters in other animals are either missing or silent in the comb jelly—except for one, the gene for the neurotransmitter glutamate. No wonder Moroz likes to call these creatures "aliens of the sea."
Instead of the typical neurotransmitter genes, the scientists found, comb jellies produce a huge diversity of receptors on the surface of their neurons. Moroz can't say yet what the receptors are doing there, but he says they're probably grabbing neurotransmitters, maybe as many as 50 to 100 neurotransmitters in all (comparable to the number of neurotransmitters in the human brain).
Rewriting Evolutionary History
The unique nature of the comb jelly nervous system led the Florida scientists to hypothesize a new evolutionary history for these marine animals, which they laid out in the Nature paper. The earliest animals, according to this new theory, had no nervous system at all. The cells of these early animals could sense their environment directly, and could send signals directly to neighboring cells.
Millions of years later, those signals and receptors became the raw material for the nervous system. But its evolution, according to Moroz, took place in two separate lineages. One led to today's ctenophores. The other led to all other animals with nervous systems—from jellyfish to us.
If there was indeed a parallel evolution with two separate lineages, the split would have happened long ago. Fossils that look a lot like modern-day ctenophores date back some 550 million years, making them among the oldest traces of complex animal life.
But precisely how and when the comb jelly split off from other animal lineages remains controversial. To draw the animal evolutionary tree, Moroz and his colleagues analyzed the similarity of DNA in different species. According to the authors, ctenophores belong to a lineage all their own that split off from the others at the tree's base.

Comb jellies, like this one at Monterey Bay Aquarium, California, are missing many genes considered essential for the development and function of neurons.

PHOTOGRAPH BY GEORGE GRALL, NATIONAL GEOGRAPHIC CREATIVE


In finding that relationship, the new paper confirms the findings of a team led byAndy Baxevanis, head of the Computational Genomics Unit at the National Human Genome Research Institute, who arrived at a similar conclusion in December after sequencing the genome of another ctenophore species, the American comb jelly (Mnemiopsis leidyi). "You couldn't ask for a better outcome," he said about Moroz's research. "It really shakes up how we think animal complexity evolved."
Gert Woerheide, an evolutionary geobiologist at Ludwig-Maximilians-Universität in Munich, who was not involved in the research, agreed that Moroz and his colleagues have made a thorough case for their revised view of brain evolution. "I think, in this respect, this is a great paper," he said.
But in terms of the actual shape of the animal family tree, Woerheide is less convinced. He isn't sure that comb jellies branched off at the base of the tree, he said; sponges, for example, might have branched off first. In Woerheide's view, the exact reconstruction of the tree reaching so far back in evolutionary history remains an open question.
No matter how the nervous systems of comb jellies evolved, though, everyone agrees that they are weird—and thus worth getting to know better. As Casey Dunn, an evolutionary biologist at Brown University in Providence, Rhode Island, who was not involved in the research, pointed out, comb jellies are turning out to be "even more different from other animals than had previously been appreciated."

Encyclopedia of the tree of life  4

Presumably, “tree of life” is placed in quotation marks because it so little resembles a tree. Didn’t it used to be capped, as Tree of Life?

Octopuses ‘are aliens’, scientists decide after DNA study 5

Not to freak you out or anything, but scientists have just revealed that octopuses are so weird they’re basically aliens.
The first full genome sequence shows of that octopuses (NOT octopi) are totally different from all other animals – and their genome shows a striking level of complexity with 33,000 protein-coding genes identified, more than in a human.
There we were thinking it was quite freaky enough when they learned how to open jam jars.
US researcher Dr Clifton Ragsdale, from the University of Chicago, said: ;The octopus appears to be utterly different from all other animals, even other molluscs, with its eight prehensile arms, its large brain and its clever problem-solving abilities.
‘The late British zoologist Martin Wells said the octopus is an alien. In this sense, then, our paper describes the first sequenced genome from an alien.’
Octopuses: What even ARE they?
They inhabit every ocean at almost all depths and possess a range of features that call to mind sci-fi aliens.
These include prehensile sucker-lined tentacles, highly mobile, camera-like eyes sensitive to polarised light, sophisticated camouflage systems that alter skin colour and patterns, jet-propulsion, three hearts, and the ability to regenerate severed limbs.
The scientists estimate that the two-spot octopus genome contains 2.7 billion base pairs – the chemical units of DNA – with long stretches of repeated sequences.

1) http://www.icr.org/article/are-rotifers-gene-stealers-or-uniquely/
2) http://www.evolutionnews.org/2008/01/darwins_failed_predictions_sli_8004654.html
3) http://news.nationalgeographic.com/news/2014/05/140521-comb-jelly-ctenophores-oldest-animal-family-tree-science/
4) http://www.uncommondescent.com/tree-of-life/encyclopedia-of-the-tree-of-life/
5) http://metro.co.uk/2015/08/12/octopuses-are-aliens-scientists-decide-after-dna-study-5339123/#ixzz3ievvjMOZ



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4 Darwin Was Wrong about the Tree of Life on Wed Dec 02, 2015 12:21 am

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Darwin Was Wrong about the Tree of Life 1

The cover story in Britain's leading science magazine, New Scientist, admits that Darwin was wrong about the tree of life. See below, Attenborough's Missing Link, for the amazingly bad timing of Sir David Attenborough's evolution pronouncement and this cover story.
2012 Update: For extraordinary excerpts from this New Scientist article, see our rebuttal to Jerry Coyne's criticism of RSR, where he wrongly indicates that the scientific evidence documented in this article "is common only in bacteria..." See this also debated by clicking on this link into Round Five of the RSR Debate with Evolutionist AronRa. This popular atheist claimed that the phylogenetic tree of life shows that evolutionary descent is doubly confirmed when re-examined genetically. Bob Enyart challenged this by referencing the many genomes that leading evolutionists admit do not fit into the predicted Darwinian pattern. In Round Five, Enyart also presents the discoveries published in peer-reviewed evolutionary journals as in RSR's List of Genomes that Just Don't Fit, and those from the New Scientist article, showing geneticists at world-renowned institutions blatantly admitting that DNA, RNA, and proteins demonstrate contradictory evolutionary pathways and therefore, via genetic science, undermine the alleged Darwinian tree of life.
2013 Update: Things are getting worse. For the rebellion against the Creator, in addition to all the genomes that just don't fit, it turns out that, according to the journal Nature, regarding the data used to identify the alleged evolutionary ancestry of tens of thousands of species, there are "holes in tree of life". Of more than 6,000 papers surveyed, 4,000 of them have no accessible data. And worse yet, while some of the data that was accessible required private correspondence with other scientists, according to the article, "Small portion of phylogenetic data is stored publicly" published at OpenTreeofLife.org, "only about four percent of [the data for] published phylogenies are stored in [publicly accessible databases" like TreeBASE. (This is not unlike the data that's gone missing for that infamous global warming hockey stick graph.)
* Testimony Contrary to Interests: The Darwinist New Scientist magazine published their cover story, Darwin Was Wrong about the Tree of Life. About this Tree of Life theory (named after the actual tree described in Genesis), the magazine reports that Darwin's theory of descent was as important as his theory of natural selection. Of the thousands of species genetically evaluated so far, more than half are not the product of a biological pathway represented by a tree (or a bush for that matter).
New Scientist Excerpts: The discoveries presented in this NS article affirm the creationist take on this and contradict the dismissive misrepresentation of evolutionists like Jerry Coyne and AronRa, who claim, respectively, that such findings are "common only in bacteria" and otherwise relegated to the "occasional odd gene", and that the article "focus[ed] primarily on microbes," whereas, for example, NS reported that a UC Davis study:
...compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, [they] should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. [They] failed. The problem was that different genes told contradictory evolutionary stories. -New Scientist
NS also reports according to the National Academy of Sciences that:
...ever more incongruous bits of DNA are turning up. Last year, for example, a team at the University of Texas… found a peculiar chunk of DNA in the genomes of eight animals [including] – the mouse, rat, …, little brown bat, … opossum, [a] lizard and [a] frog – but not in 25 others [where Darwin's tree would have it], including [in] humans, elephants, chickens and fish.
As creationists, we predict that the “common only in bacteria” argument will go the way of Junk DNA, as the New Scientist article showed:
Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates.
Biologist Michael Syvanen of the University of California said that, "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another… We've just annihilated the tree of life. It's not a tree any more…"
But today the project [to reconstruct the tree] lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says [an evolutionary biologist from Marie Curie University in Paris, Eric] Bapteste.
RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.
And to make matters worse, protein sequencing might suggest yet a third evolutionary pathway, and then all of these were producing trees that contradicted the traditional pathways based on fossil evidence and anatomy.
Far from New Scientist's evidence referring primarily to microorganisms and only an occasional tip of a branch on the tree, the landmark article mentions single-celled organisms only to show that what is known of them is also common for organisms throughout the tree of life:
Having uprooted the tree of unicellular life, biologists are now taking their axes to the remaining branches.
And when they report something that Coyne and AronRa suggest is the articles primary evidence, that prokaryotes (organisms without a nucleus) cannot be fit to Darwin's hierarchical tree of life, they do so only to explain that this is the rule for eukaryotes, which would include all plants and animals. For example, as reported in NS and in the Proceedings of the National Academy of Sciences, European researchers:
…examined more than half a million genes from 181 prokaryotes and found that 80 per cent of them showed signs of horizontal transfer [i.e., not Darwinian hierarchy]. Surprisingly, HGT also turns out to be the rule rather than the exception in the third great domain of life, the eukaryotes. -New Scientist
* 2014 Update: And things just keep getting worser. Because Darwin was wrong about the tree of life, creationists expect that his tree concept lacks predictive value. Here's an example where avowed Darwinists provide evidence that we creationists are correct. As reported by LiveScience, According to researchers running a major National Science Foundation evolution experiment, "If Darwin was right", they would have documented the evidence for his claimed insight on competition and the tree of life. Instead, their results falsified Darwin's claim. Of the 60 species of algae being studied for a five year period, Charles Darwin predicted how well and how poorly such organisms would compete for resources, based on their respective distances from each other on the (supposed) tree of life. But of the outcome, "It was completely unexpected. We sat there banging our heads against the wall. Darwin's hypothesis has been with us for so long, how can it not be right? ... We should be able to look at the Tree of Life, and evolution should make it clear who will win in competition and who will lose. But the traits that regulate competition can't be predicted from the Tree of Life." Interestingly, after scores of science sites, including RichardDawkins.net, reported on the LiveScience article, titled Doubting Darwin: Algae Findings Surprise Scientists, the politically correct editors at LS renamed the piece to something less offensive. 


* Shock Chimp Y Chromosome Report, 30% Different: [As discussed in another RSR show, check out this post-show note.] Geneticists have sequenced the chimpanzee's Y chromosome has been sequenced,  the evolutionists are in "shock" once again. See the April 2011Creation Magazine and their online report about team leader Dr. David Page of the Whitehead Institute for Biomedical Research in Cambridge, Mass., said in the journal Nature (1-14-2010), that the human and chimp Y chromosomes are "horrendously different from each other." Horrendously? A_O, is that a scientific term? Why not just, "different?" Why horrendously so? Because for modern Darwinism to not lose face, chimps have to be shown to be our closest relatives. Yet the chimp's Y chromosome (that which makes us reproducing males... well, males...):
- has only 66% of the genes that we do
- codes for only half the proteins ours does
- has 30% of the entire Y that can't be aligned to our Y
- and the human Y has 30% that doesn't line up to the chimps.






* Sequencing of Marine Worm Kills Common Ancestor of Man and Insects: Molecular biology has removed from it's perch the long-alleged common ancestor of insects and humans, the marine worm acoelomorphs. According to LiveScience, "the missing link has gone missing" as reported in the Jan/Feb 2011 Creation Matters:
- marine worms are more closely related to humans than are mollusks and insects - Nature 2-9-11
- Evolution: A can of worms. Nature 2-9-11
- "the missing link has gone missing" Dept. of Genetics & Evolution's Max Telford, Univ. College, London
- evolutionists "alarmed" with "vehemence" - Nature magazine
- shows how important these worm props were to the evolutionary story-telling
- "the most politically fraught paper I've ever written" -Genetic researcher Max Telford
- Acoelomorpha Flatworm formerly known as common man-bug ancestor

Political? Yes, political.

* Related RSR Reports: See our reports on the fascinating DNA sequencing results from the roundworms, kangaroos, and sponges! And see the University of Chicago's famed evolutionist, Jerry Coyne, claim that the nonconformist genomes are relegated to the realm of microorganisms, which misunderstanding is falsified in the RSR rebuttal to Jerry Coyne's criticism of Bob Enyart.
* Dawkins Proves a Creationist Right and the Above Report Proves Dawkins Wrong: Richard Dawkins proves a creationist right in this 80-second video regarding an extremely bold claim that none of Dawkins' books provided evidence for evolution. And the above shows that Dawkins is wrong in his "interview" with creationist Wendy Wright when he claims that DNA shows a systematic hierarchy of relationships that supposedly document Darwin's tree of life.

* Two Strikes: David Attenborough's Missing Link and Darwin's Tree: It was with terrible timing that Sir David Attenborough concluded his new BBC special saying, "So now we can trace the ancestry of all animals in the tree of life and demonstrate the truth of Darwin[...]" Ha! Coincidentally to the publication of the New Scientist cover story, the BBC was vastly overselling a very pretty fossil that is likely to become [update: and has already become] an evolutionary dud. Over the decades, whenever some especially interesting monkey or ape fossil is revealed, the public is told that the missing link is finally found. Now a fossil monkey Ida, erroneously dated at 47-million-years too old, is presented by evolutionist Attenborough. He pretends to quote skeptics asking: "'We are primates, show us the link?' The link they would have said up to now is missing - well it's no longer missing." And in a related story, Attenborough's recent BBC special, Charles Darwin and the Tree of Life, had its conclusion exactly wrong. For as his latest devotion to Darwin's tree was preparing to air, New Scientist was cutting it down.
* Hey! Not So Slow: This was an earlier presentation of what became our List of Not So Old Things, RSF's growing list of scientific observations that undermine traditional evidence for million-year ages. KGOV.com's Real Science Radio hostsFred Williams and Bob Enyart list physical evidence against old-age claims including that many atheistic, old-earth geologists no longer claim formation over millions of years for many major features of the earth's surface. 2012 Update: RSF's List inspired its own website, YoungEarth.com! Check it out!
Today's Resource: Have you browsed through our Science Department in the KGOV Store? Check out especially Walt Brown's In the Beginning and Bob's interviews with this great scientist in Walt Brown Week! You'll also love Dr. Guillermo Gonzalez' Privileged Planet(clip), and Illustra Media's Unlocking the Mystery of Life (clip)! You can consider our BEL Science Pack; Bob Enyart's Age of the Earth Debate; and the superb kids' radio programming, Jonathan Park: The Adventure Begins! And Bob strongly recommends that you subscribe to CMI's tremendous Creation magazine!

Charles Darwin's tree of life is 'wrong and misleading', claim scientists

They believe the concept misleads us because his theory limits and even obscures the study of organisms and their ancestries. Evolution is far too complex to be explained by a few roots and branches, they claim. In Darwin's The Origin of Species, published in 1859, the British naturalist drew a diagram of an oak to depict how one species can evolve into many. But not much was known about primitive life forms or genetics back then when he was only dealing with plants and animals – long before there was any real comprehension of DNA or bacteria.Researchers say although for much of the past 150 years biology has largely concerned itself with filling in the details of the tree it is now obsolete and needs to be discarded.

Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: "For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality." The discovery of the structure of DNA in 1953 – whose pioneers believed it would provide proof of Darwin's tree – opened up new vistas for evolutionary biology. But current research is finding a far more complex scenario than Darwin could have imagined – particularly in relation to bacteria and single-celled organisms. These simple life forms represent most of Earth's biomass and diversity – not to mention the first two-thirds of the planet's history. Many of their species swap genes back and forth, or engage in gene duplication, recombination, gene loss or gene transfers from multiple sources. Dr John Dupré, a philosopher of biology at Exeter University, said: "If there is a tree of life it's a small irregular structure growing out of the web of life." More fundamentally recent research suggests the evolution of animals and plants isn't exactly tree-like either. Dr Dupré said: "There are problems even in that little corner." Having uprooted the tree of unicellular life biologists are now taking their axes to the remaining branches. Dr Bapteste said: "If you don't have a tree of life what does it mean for evolutionary biology. At first it's very scary – but in the past couple of years people have begun to free their minds." Both he and co-researcher Dr Ford Doolittle stressed that downgrading the tree of life doesn't mean the theory of evolution is wrong just that evolution is not as tidy as we would like to believe. Dr Doolittle, of California University, said: "We should relax a bit on this. We understand evolution pretty well it's just it is more complex than Darwin imagined. The tree isn't the only pattern." But others see the uprooting of the tree of life as the start of something bigger, reports New Scientist. Dr Dupré said: "It's part of a revolutionary change in biology. Our standard model of evolution is under enormous pressure. We're clearly going to see evolution as much more about mergers and collaboration than change within isolated lineages." Understanding how cells evolve and mutate is incredibly important it's helping scientists learn why some diseases are resistant to vaccines and antibiotics, and why others can evade the immune system. It's leading to environmental solutions too some bacterial genes can break down harsh contaminants such as benzene into harmless by-products. Dr Rose said: "The tree of life is being politely buried – we all know that. What's less accepted is our whole fundamental view of biology needs to change." He says biology is vastly more complex than we thought and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century. Dr Bapteste said: "The tree of life was useful. It helped us to understand evolution was real. But now we know more about evolution it's time to move on." Darwin's model is no stranger to controversy. It has played a key role in the much larger debate with creationists who are convinced life on Earth is so complex it could only have come about from intelligent design – in other words, the hand of God.


New mechanism of evolution — POOF

Each species has large numbers of unique genes that seem to have magically arisen without any ancestor. Evolutionists are saying they essentially POOFed into existence. These genes are referred to as ORFans or orphan genes. From the Max Plank Institute:


However, with the advent of sequencing of full genomes, it became clear that approximately 20–40% of the identified genes could not be associated with a gene family that was known before. Such genes were originally called ‘orphan’ genes

Evolutionary Origin of Orphan Genes




20-40% of the genes discovered cannot be explained by common ancestry or common descent. So what mechanism is left to explain it? Special creation? But evolutionists can’t accept special creation, so they just pretend they’ve made a discovery of a new mechanism of evolution that can work just as well. They haven’t given it a name yet, so let us call it POOF. What is POOF? POOF is the mechanism by which proteins can easily arise out random nucleotide sequences like a poem can emerge out of randomly tossed scrabble letters. I bold one of their euphemisms for the POOF mechanism in the following paragraph:


Orphan genes may have played key roles in generating lineage specific adaptations and could be a continuous source of evolutionary novelties. Their existence suggests that functional ribonucleic acids (RNAs) andproteins can relatively easily arise out of random nucleotide sequences, although these processes still need to be experimentally explored.


The reasoning they use goes like this, “we have all these genes that can’t be explained by slight successive modifications, so they must have arisen spontaneously out of nowhere. Because evolution is fact, this implies evolution can just take random material and create functional systems in a flash. We’ve made a fabulous discovery about the miracles of evolution even though we can’t demonstrate it experimentally.”


Experiments actually refute such assertions, but that won’t stop evolutionists from promoting demonstrably false ideas as some new discovery! And it’s not only the genes but the regulatory mechanisms that poof into existence:


On the other hand, there is now little doubt that new genes have arisen throughout the phylogenetic history and the general model of de novo evolution of genes appears to be well supported by now. However, this also raises several new questions. The foremost one is the question of how new promotors with a defined regulation can arise.



“de novo evolution of genes” is also another euphemism for the POOF mechanism.
But it’s not just the genes and regulatory regions, but also developmental mechanisms that deploy these novelties to create radical new species (like multicellular ones from single cellular ones).

gene lists can be associated with major evolutionary steps, such as the origin of germ layers, or the origin of multicellularity . Interestingly, this approach showed also that younger genes tend to be increasingly more developmentally regulated compared with evolutionary older genes



Not only do the orphan genes emerge, they emerge with the most infrastructure to integrate them into the POOFED species. So genes, proteins, and developmental mechanisms, and new species also POOFED into existence. They sound almost like closet creationists!
The evolutionists conclude, evolution can do far more than we ever supposed because evolution can POOF thousands of genes and regulatory mechanisms into sudden existence rather than through slight successive modifications of an ancestor. What a wonderful discovery. 

NOTES
1. Behe, who accepts common descent, is said to have jokingly used the phrase, “puff of smoke” to describe the mechanism that can create irreducible complexity. In internet debates, the phrase got converted to “POOF” to emphasize the magical character of the mechanism. It seems now, evolutionary biologists are seriously resorting to Behe’s POOF mechanism whether they want to admit it or not.
How did Behe arrived at the POOF mechanism which evolutionary biologists are now only discovering?


I lectured at Hillsdale College as part of a week-long lecture series on the intelligent design debate. After Michael Behe’s lecture, some of us pressed him to explain exactly how the intelligent designer created the various “irreducibly complex” mechanisms that cannot–according to Behe–be explained as products of evolution by natural selection. He repeatedly refused to answer. But after a long night of drinking, he finally answered: “A puff of smoke!”
Larry Arnhart
http://darwinianconservatism.blogspot.com/2006/09/has-anyone-seen-evolution.html




2. Orphan genes have made the Irreducible Complexity argument that much stronger.




1) http://kgov.com/darwin-was-wrong-about-the-tree-of-life
2) http://www.telegraph.co.uk/news/science/4312355/Charles-Darwins-tree-of-life-is-wrong-and-misleading-claim-scientists.html
3) http://www.uncommondescent.com/genetics/new-mechanism-of-evolution-poof/

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Study takes close look at formidable camel spider jaws 1

"Our limited understanding of the incredible jaws of these arachnids, together with terminology that is unstandardized and even contradictory, has hindered our ability to classify them and figure out where they fit in the arachnid tree of life because, much like the cranial anatomy of vertebrates, the jaws of solifuges contain most of the relevant information," said Lorenzo Prendini, a curator in the Museum's Division of Invertebrate Zoology and an author on the paper. "The last time there was a major publication of this kind on camel spiders was in 1934, which, considering how conspicuous and ubiquitous they are in some parts of the world, is almost unbelievable."

For the first time, researchers have created a visual atlas and dictionary of terms for the many strange features on the fearsome-looking jaws of a little known group of arachnids. Called camel spiders, baardskeerders [beard-cutters], sun spiders, wind scorpions, and other colorful names, Solifugae are an order of arachnids that are neither spiders nor scorpions. Their jaws, or chelicerae, are the largest for body size among the group of animals that possess these specialized mouthparts—including horseshoe crabs, sea spiders, and arachnids—and bear most of the structures used for their classification. Despite their prominence in folklore around the world, solifuges have scarcely been studied, and much remains unknown about their biology.
In research out today in the Bulletin of the American Museum of Natural History, scientists from the Museum, the National Museum of Namibia, and Texas A&M University present the first comprehensive analysis of jaw morphology acrossSolifugae.
"Our limited understanding of the incredible jaws of these arachnids, together with terminology that is unstandardized and even contradictory, has hindered our ability to classify them and figure out where they fit in the arachnid tree of life because, much like the cranial anatomy of vertebrates, the jaws of solifuges contain most of the relevant information," said Lorenzo Prendini, a curator in the Museum's Division of Invertebrate Zoology and an author on the paper. "The last time there was a major publication of this kind on camel spiders was in 1934, which, considering how conspicuous and ubiquitous they are in some parts of the world, is almost unbelievable."
There are about 1,100 species of camel spiders, which range in size from tiny, a few millimeters long, to about 15 centimeters (six inches) in length. The arachnids look like big, hairy spiders with an extra pair of legs—which are really pedipalps, leg-like structures ending in an adhesive sucker, and used like arms for grasping, holding, and climbing. Mostly found in dry environments, solifuges are abundant in the savannas, steppes, and deserts of Africa, the Middle East, central Asia, the southwestern United States, Mexico, and South America. They differ most obviously from their spider and scorpion relatives in three ways: their massive two-segmented jaws, which can be up to one-third of their body length and are armed with teeth and spine-like and horn-like processes of various sizes; the flagellum, found on the jaws of adult males in most species and thought to play a major role in reproduction; and the malleoli, racquet-shaped sensory organs on the underside of the first segment of the last pair of legs.







This image shows the jaws of camel spiders in the family Solpugidae. Prolateral (inner) side in left column; retrolateral (outer) side in right column. Note, males have flagellum, females do not. A, B. Zeria carli, male; C-F. Zeria lawrencei, male (C, D) and female (E, F); G, H. Zeria venator, male. Credit: © Tharina Bird
"In most solifuge families, species identification is based primarily on features of the jaws, yet no comprehensive survey of these character systems has ever been done," said Tharina Bird, a senior curator at the National Museum of Namibia and lead author of the paper.
Bird, Prendini, and co-author Robert Wharton, a professor at Texas A&M University, studied the jaws of 188 camel spider species representing all solifuge families from historical collections at the Museum and elsewhere, including material collected during expeditions by Prendini and Bird over the past decade—no easy feat. These arachnids, nicknamed the "Kalahari Ferrari," can reach speeds up to 10 miles per hour and generally only come out at night during the warm season, although some species are active only during the mid-day heat.
"Camel spiders are extremely difficult to collect and study, which may explain why they are so poorly known," Prendini said. "They're very seasonal, short-lived, and fast-moving animals. Many live in the hottest, driest, and most dangerous places in the world, and usually only the adult males can be identified to species with any confidence."
Combining observations from high-resolution microscopy of the specimens' jaws with existing literature, the researchers proposed nearly 80 terms—many of them new—for structures of similar appearance and position, to serve as common language for future work. Mucron organ, for instance, refers to a small, circular organ on the side of the mucron, or toothless section of the upper jaw, and which turned out to be common in solifuges although it had never been mentioned before. Or flagellar shaft, an elongated, variously shaped portion of the flagellum found in many species, which contains two canals, one with an external opening thought to secrete a fluid which plays a part in reproduction.







This image shows the variety of arachnids in the order Solifugae: A. (female) and B. (male) Galeodes caspius fuscus, Kazakhstan; C. Rhagodes sp., Kenya; D. Rhagodes sp., India; E. Hexisopus sp., Namibia; F. Chelypus sp., South Africa; G. Metasolpuga picta, Namibia; H. Zeria sericea, Namibia. Credit: © Alexander Gromov (A, B), Simon van Noort (C), Sanjay Das (D), Telané Greyling (E), Christian Boix-Hinzen (F), Tharina Bird (G, H)
"It's really vital that everyone be on the same page in terms of scientific language about this group," Bird said. "That way, if I'm describing a particular structure, e.g. a tooth, of a species I found in Africa, someone who sees a similar structure on a species in China can accurately determine if it is the same structure, and can communicate about it unambiguously."
In doing this work, the researchers made several important discoveries about the flagellum of male camel spiders. This unique structure can look very different among species—from long, thin, and whip-like to short, stout and spoon-shaped, flat and blade-like, or even concave and bowl-shaped. But it is homologous, meaning that it has a single origin in the common ancestor ofSolifugae. Although the flagellum, along with the rest of the jaw, is thought to play an important role in the mating behavior of camel spiders, and was observed to transfer sperm to the female in at least one species, little is known about its precise function.
"We lack data because hardly anyone can keep camel spiders alive long enough to breed them in captivity, and observing solifuges mating in the wild is even more difficult," Prendini said. "They are high-octane creatures, they burn out quickly. So, there are still many unknowns about how they live."

1) http://phys.org/news/2015-06-formidable-camel-spider-jaws.html

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Horizontal Gene transfer, another ad hoc explanation

The evidence of jumping transposons (=a segment of DNA that can become integrated at many different sites along a chromosome)
Common Ancestry
1. In recent years, evolutionary biologists have increasingly used DNA sequences to construct evolutionary trees. Researchers find transposons particularly suitable for this endeavor.
2. When evolutionary biologists propose evolutionary relationships, they rely on the principle that organisms with shared DNA sequences arise from a common ancestor.
3. But other mechanisms exist that can introduce the identical DNA sequences. Horizontal gene transfer (HGT) is one.
Horizontal Gene Transfer (HGT) Mimics Common Ancestry
4. HGT refers to any process that transfers genetic material to another organism without the recipient being the offspring of the donor. HGT occurs frequently in bacteria and archaea. A consequence of this process is that, from an evolutionary vantage point, microbes that are unrelated through common descent will possess the same DNA sequences. In other words, HGT has the same genetic signature as common ancestry.
5. Until recently, most biologists thought that HGT was confined to microbes. Yet, in the last couple of years, researchers have uncovered evidence for horizontal gene transfer in higher plants and animals, which they think is mediated by viruses and single-celled pathogens transmitted from species to species via an insect vector. Because of transposons’ mobility within genomes, they readily take part in HGT events.
6. As with microbes, HGT in higher plants and animals obfuscates the ability of evolutionary biologists to use transposons to establish reliable evolutionary relationships.
7. For example, researchers discovered that when they use two different classes of transposons, called BovB and Spin elements, to build evolutionary trees, absurd relationships resulted. Cows were more closely related to snakes than to elephants and geckos more closely related to horses than to other lizards.
8. Many people regard shared DNA sequences as the best evidence for evolution and common descent. But as this cutting-edge research demonstrates, other mechanisms, such as horizontal gene transfer, can introduce the same DNA sequences in organisms, thus, masquerading as evidence for common descent of HGT.
9. As science continues to unmask understanding of these processes, the case for common design strengthens.
10. The ability of transposons to jump around or move from the genome of one organism into that of another is an evidence for a common designer of all species who is God.
11. God exists.

Shared Genes Undercut Evolutionary Tree 

In a study published in Current Biology, Vanderbilt University evolutionary biologists Antonis Rokas and Jason Slot examined two different species of mold that have distinct DNA and appearances. Strangely, however, these molds share a sequence of 60 thousand base pairs, lined up in the same orde
r.

This sequence contains a cluster of genes that, when translated by its cell into proteins, forms an assembly line to manufacture a particular chemical used for defense. Since the chances are nil that the exact same sequence of 60 thousand bases twice evolved through any random approach, the researchers assumed that the whole cluster "jumped" from one fungus to the other.

Other researchers have observed similar "gene jumping" across species in microbes, which are equipped with tools that sample and incorporate DNA from their environments into their super-small, single cells. But no known mechanism for this process—called "horizontal gene transfer" or "lateral gene transfer (LGT)"—has been characterized for eukaryotes (cells with nuclei and specialized structures), let alone for multicellular eukaryotes such as fungi, slugs, or four-footed animals.

Horizontal gene transfer in evolution: facts and challenges

it is a disputed point whether horizontal gene transfer precludes the reconstruction of phylogenetic relationships in the microbial world. In any case, horizontal gene transfer is not a canonical or typical evolutionary mechanism. Thus, I agree with other authors that there is a need for a new paradigm in evolution that includes horizontal gene transfer among other neo-Darwinian and non-neo-Darwinian mechanisms.

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Molecular Biology Has Failed to Yield a Grand "Tree of Life"

When fossils failed to demonstrate that animals evolved from a common ancestor, evolutionary scientists turned to another type of evidence -- DNA sequence data -- to demonstrate a tree of life. In the 1960s, around the time the genetic code was first understood, biochemists Émile Zuckerkandl and Linus Pauling hypothesized that if DNA sequences could be used to produce evolutionary trees -- trees that matched those based upon morphological or anatomical characteristics -- this would furnish "the best available single proof of the reality of macro-evolution."99 Thus began a decades-long effort to sequence the genes of many organisms and construct "molecular" based evolutionary ("phylogenetic") trees. The ultimate goal has been to construct a grand "tree of life," showing how all living organisms are related through universal common ancestry.
The Main Assumption
The basic logic behind building molecular trees is relatively simple. First, investigators choose a gene, or a suite of genes, found across multiple organisms. Next, those genes are analyzed to determine their nucleotide sequences, so the gene sequences of various organisms can then be compared. Finally, an evolutionary tree is constructed based upon the principle that the more similar the nucleotide sequence, the more closely related the species. A paper in the journal Biological Theory puts it this way:
[M]olecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness.100
This assumption is essentially an articulation of a major feature of the theory - the idea of universal common ancestry. Nonetheless, it's important to realize that it is a mere assumption to claim that genetic similarities between different species necessarily result from common ancestry.
Operating strictly within a Darwinian paradigm, these assumptions flow naturally. As the aforementioned Biological Theory paper explains, the main assumption underlying molecular trees "derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change."101 So the theory is assumed to be true to construct a tree. But also, if Darwinian evolution is true, construction of trees using different sequences should reveal a reasonably consistent pattern across different genes or sequences.
This makes it all the more significant that efforts to build a grand "tree of life" using DNA or other biological sequence data have not conformed to expectations. The basic problem is that one gene gives one version of the tree of life, while another gene gives a highly different, and conflicting, version of the tree. For example, as we'll discuss further below, the standard mammalian tree places humans more closely related to rodents than to elephants. But studies of a certain type of DNA called microRNA genes have suggested the opposite -- that humans were closer to elephants than rodents. Such conflicts between gene-based trees are extremely common.
The genetic data is thus not painting a consistent picture of common ancestry, showing the assumptions behind tree-building commonly fail. This leads to justifiable questions about whether universal common ancestry is correct.
Conflicts in the Base of the Tree of Life
Problems first arose when molecular biologists sequenced genes from the three basic domains of life -- bacteria, archaea, and eukarya -- but those genes did not allow these basic groups of life to be resolved into a treelike pattern. In 2009, the journal New Scientist published a cover story titled, "Why Darwin was wrong about the tree of life" which explained these quandaries:
The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.102
This sort of data led biochemist W. Ford Doolittle to explain that "Molecular phylogenists will have failed to find the 'true tree,' not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree."103 New Scientist put it this way: "For a long time the holy grail was to build a tree of life ... But today the project lies in tatters, torn to pieces by an onslaught of negative evidence."104
Many evolutionists sometimes reply that these problems arise only when studying microorganisms like bacteria -- organisms which can swap genes through a process called "horizontal gene transfer," thereby muddying the signal of evolutionary relationships. But this objection isn't quite true, since the tree of life is challenged even among higher organisms where such gene-swapping is not prevalent. Carl Woese, a pioneer of evolutionary molecular systematics, explains:
Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.105
Likewise, the New Scientist article notes that "research suggests that the evolution of animals and plants isn't exactly tree-like either."106 The article explains what happened when microbiologist Michael Syvanen tried to create a tree showing evolutionary relationships using 2000 genes from a diverse group of animals:
He failed. The problem was that different genes told contradictory evolutionary stories. ... the genes were sending mixed signals. ... Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another.107
The data were so difficult to resolve into a tree that Syvanen lamented, "We've just annihilated the tree of life."108 Many other papers in the technical literature recognize similar problems.
Conflicts Between Higher Branches
A 2009 paper in Trends in Ecology and Evolution notes that, "A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome."109 Similarly, a paper in Genome Research studied the DNA sequences in various animal groups and found that "different proteins generate different phylogenetic tree[s]."110 A June, 2012 article in Nature reported that short strands of RNA called microRNAs "are tearing apart traditional ideas about the animal family tree." Dartmouth biologist Kevin Peterson who studies microRNAs lamented, "I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree." According to the article, microRNAs yielded "a radically different diagram for mammals: one that aligns humans more closely with elephants than with rodents." Peterson put it bluntly: "The microRNAs are totally unambiguous ... they give a totally different tree from what everyone else wants."111
Conflicts Between Molecules and Morphology
Not all phylogenetic trees are constructed by comparing molecules like DNA from different species. Many trees are based upon comparing the form, structure, and body plan of different organisms -- also called "morphology." But conflicts between molecule-based trees and morphology-based trees are also common. A 2012 paper studying bat relationships made this clear, stating: "Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."112 This is hardly the only study to encounter conflicts between DNA-based trees and trees based upon anatomical or morphological characteristics. Textbooks often claim common descent is supported using the example of a tree of animals based upon the enzyme cytochrome c which matches the traditional evolutionary tree based upon morphology.113 However, textbooks rarely mention that the tree based upon a different enzyme,cytochrome b, sharply conflicts with the standard evolutionary tree. As one article in Trends in Ecology and Evolution observed:
[T]he mitochondrial cytochrome b gene implied . . . an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.114
Strikingly, a different article in Trends in Ecology and Evolution concluded, "the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent [evolutionary relationship] probably being the grouping of elephants and sea cows."115 Because of such conflicts, a major review article in Nature reported, "disparities between molecular and morphological trees" lead to "evolution wars" because "[e]volutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."116
Finally, a study published in Science in 2005 tried to use genes to reconstruct the relationships of the animal phyla, but concluded that "[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved." The following year, the same authors published a scientific paper titled, "Bushes in the Tree of Life," which offered striking conclusions. The authors acknowledge that "a large fraction of single genes produce phylogenies of poor quality," observing that one study "omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom." The paper suggests that "certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available." The paper even contends that "[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics."117
Unfortunately, one assumption that these evolutionary biologists aren't willing to re-evaluate is the assumption that universal common ancestry is correct. They appeal to a myriad of ad hoc arguments -- horizontal gene transfer, long branch attraction, rapid evolution, different rates of evolution, coalescent theory, incomplete sampling, flawed methodology, and convergent evolution -- to explain away inconvenient data which doesn't fit the coveted treelike pattern. As a 2012 paper stated, "phylogenetic conflict is common, and frequently the norm rather than the exception."118 At the end of the day, the dream that DNA sequence data would fit into a nice-neat tree of life has failed, and with it a key prediction of neo-Darwinian theory.


http://www.evolutionnews.org/2015/02/problem_6_molec091151.html

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The new biology: beyond the Modern Synthesis


analyses of newly abundant sequence data in the late 20th Century showed that rather than a highly congruent coalescence of genes at the times of speciation events, the coalescence times of alleles among species are highly variable. As such, species trees and gene trees often cannot be equated


1) http://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-2-30

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Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth

1

The most serious problem of Theobald’s analysis is that he used aligned sequences compiled by Brown et al. [1], who were interested in resolving the phylogenetic relationships among archaebacteria, eubacteria, and eukaryotes, including whether each domain of life constitutes a monophyletic clade. So they a priory assumed the existence of UCA. Indeed, alignment is a procedure based on an assumption that the sequences have diverged from a common ancestral sequence.

1.https://www.hindawi.com/journals/tswj/2012/479824/

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http://darwins-god.blogspot.com.br/2014/05/evolution-professor-biological-designs.html

This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is “no known mechanism or function that would account for this level of conservation at the observed evolutionary distances.” Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are “astonishing.”

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"Each new prokaryotic genome that appears contains dozens, if not hundreds, of genes not found in the genomes of its nearest sequenced relatives but found elsewhere among Bacteria or Archaea."
W. Ford Doolittle Science 286, 1999.

http://www.unm.edu/~hdelaney/moleculartrees.html

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Prokaryotic evolution and the tree of life are two different things

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761302/

The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.

The network of life: genome beginnings and evolution

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874017/

The rapid growth of genome-sequence data since the mid-1990s is now providing unprecedented detail on the genetic basis of life, and not surprisingly is catalysing the most fundamental re-evaluation of origins and evolution since Darwin’s day. Several papers in this theme issue argue that Darwin’s tree of life is now best seen as an approximation—one quite adequate as a description of some parts of the living world (e.g. morphologically complex eukaryotes), but less helpful elsewhere (e.g. viruses and many prokaryotes); indeed, one of our authors goes farther, proclaiming the “demise” of Darwin’s tree as a hypothesis on the diversity and seeming naturalness of hierarchical arrangements of groups of living organisms.

Uprooting the Tree of Life

http://labs.icb.ufmg.br/lbem/aulas/grad/evol/treeoflife-complexcells.pdf

Charles Darwin contended more than a century ago that all modern species diverged from a more limited set of ancestral groups, which themselves evolved from still fewer progenitors and so on back to the beginning of life. In principle, then, the relationships among all living and extinct organisms could be represented as a single genealogical tree.Most contemporary researchers agree. Many would even argue that the general features of this tree are already known, all the way down to the root—a solitary cell, termed life’s last universal common ancestor, that lived roughly 3.5 to 3.8 billion years ago. The consensus view did not come easily but has been widely accepted for more than a decade. Yet ill winds are blowing. To everyone’s surprise, discoveries made in the past few years have begun to cast serious doubt on some aspects of the tree, especially on the depiction of the relationships near the root.

http://youngearth.com/marine-worm-infects-trunk-darwins-tree-be-felled-soon
marine worms are more closely related to humans than are mollusks and insects - Nature 2-9-11



Last edited by Admin on Sun Jan 22, 2017 7:20 pm; edited 1 time in total

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Thanks to Peter Berean

Evidence that Large-Scale Evolution is FALSE.
-------------------------------------------------------------------------
P1. If Naturalistic-Atheistic Large-Scale Evolution (NALSE) is true, then each and every single species (present or past) is just the tip of a branch on a Single unique Universal historical Tree of Life.
P2. And, the history of that species (and its ancestors) would constitute deeper segments of that continuous branch on that Single Universal Tree of Life.
P3. Given these (P1 & P2), all of the genes from any given species should ALL tell the same story about that Single Universal Tree of Life. I.e., they should ALL indicate the same common history (for that species) and the same common location (for that species) on the tree of life.
P4. In that case, 1070 genes (that were analyzed) from 20+ different yeast species should ALL tell the same story about that Single Universal Tree of Life.
P5. So, analysis of the 1070 genes (across the 20+ species) should show us ONE Single Universal Tree of Life.
P6. They should NOT show us 1070 different Alleged Trees of Life. If they do so, this would be evidence that the single-tree-of-life hypothesis that is the CORE of Neo-Darwinian Evolution is FALSE.
P7. And the Concatenated Tree of Life (i.e., the Tree of Life that is statistically generated by using ALL of the 1070 genes together, rather than individually and separately to each generate a Tree of Life) should match the 1070 separate single Trees of Life that are individually generated from each of the separate genes.
P8. The Evidence shows that the expectations of P6 are FALSIFIED. The 1070 genes that were analyzed (from the 20+ yeast species) resulted in 1070 DIFFERENT Alleged Trees of Life. NONE of the trees of life matched each other.
-----------------------------------------------------------------------------
CONCLUSION
-----------------------------------------------------------------------------
C1. This means that the single-tree-of-life hypothesis that is the CORE of Neo-Darwinian Large-Scale Evolution is FALSE.
C2. Therefore, it is a Reasonable and Rational Inference that Neo-Darwinian Naturalistic-Atheistic Large-Scale Evolution (NALSE) is FALSE.
-----------------------------------------------------------------------------
ARGUMENT (continued)
-----------------------------------------------------------------------------
P9. The Evidence shows that the expectations of P7 are FALSIFIED. The Concatenated Tree of Life (i.e., the Tree of Life that is statistically generated by using ALL of the 1070 genes together, rather than individually and separately to generate each Tree of Life) does NOT match ANY of the 1070 separate single Trees of Life that are individually generated from each of the separate genes.
-----------------------------------------------------------------------------
CONCLUSION
-----------------------------------------------------------------------------
C3. This means that the single-tree-of-life hypothesis that is the CORE of Neo-Darwinian Large-Scale Evolution is FALSE.
C4. Therefore, it is a Reasonable and Rational Inference that Neo-Darwinian Naturalistic-Atheistic Large-Scale Evolution (NALSE) is FALSE.
-----------------------------------------------------------------------------
EVIDENCE:
-----------------------------------------------------------------------------
Quote (discussing [1] below) --> One phylogenetic study attempted to compute the evolutionary tree relating a couple dozen yeast species using 1,070 genes. The tree that uses all 1,070 genes is called the concatenation tree. They then repeated the computation 1,070 times, for each gene taken individually. Not only did none of the 1,070 trees match the concatenation tree, they also failed to show even a single match between themselves. In other words, out of the 1,071 trees, there were zero matches. It was “a bit shocking” for evolutionists, as one explained: “We are trying to figure out the phylogenetic relationships of 1.8 million species and can’t even sort out 20 yeast.”
What is interesting is how this false prediction was accommodated. The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene.
These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes that gave the right evolutionary answer. They described those genes as having “strong phylogenetic signal.” (thanks to Zaur Guchetl)
-------------------------------------------------------
REFERENCE:
-------------------------------------------------------
[1] Salichos L1, Rokas A., Nature. 2013 May 16;497(7449):327-31. doi: 10.1038/nature12130. Epub 2013 May 8. Inferring ancient divergences requires genes with strong phylogenetic signals.
[2] Quote (abstract from [1]): "To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences."

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Common Descent (Darwinism)–Science or Pseudoscience?

http://whoisyourcreator.com/topics/common-descent-darwinism-science-or-pseudoscience/

Common Descent (Darwinism)–Science or Pseudoscience?
Genetic variations can produce observable changes in existing features or traits (microevolution), but there is NO empirical evidence that reflects a new feature appearing which has never been seen before in that organism (macroevolution):

“In each of these pivotal nexuses in life’s history, the principal “types” seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate “grades” or intermediate forms between different types are detectable.”
“The Biological Big Bang model for the major transitions in evolution,” Eugene V Koonin, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, in Biology Direct 2007, 2:21.
http://www.biology-direct.com/content/2/1/21
“It is not necessarily easy to ‘see’ macroevolutionary history; there are no firsthand accounts to be read. Instead, we reconstruct the history of life using all available evidence: geology, fossils, and living organisms.”
University of California Museum of Paleontology and the National Center for Science Education’s website, “Understanding Evolution: “What is macroevolution?” page.
http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_48
Let’s examine the typical indoctrination techniques used by evolutionary groups, this one being “29+ Evidences for Macroevolution” from TalkOrigins:http://www.talkorigins.org/faqs/comdesc/section1.html

Their first three ‘evidences’ include “The fundamental unity of life”, “A nested hierarchy of species”, and the “Independent determination of the historical phylogeny.” The “unity of life” describes a common creator (God), “nested hierarchy” is the arbitrarily-devised evolutionary history of groups of organisms, and the outdated “phylogenetic tree” has now be shown to be “wrong and misleading”:
“Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: ‘For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality.’ …
Dr Rose said: ‘The tree of life is being politely buried – we all know that. What’s less accepted is our whole fundamental view of biology needs to change.’”
Telegraph UK Online, “Charles Darwin’s tree of life is ‘wrong and misleading’, claim scientists”, January 22, 2009.
http://www.telegraph.co.uk/science/4312355/Charles-Darwins-tree-of-life-is-wrong-and-misleading-claim-scientists.html

The forth ‘evidence’ is called “Intermediate and transitional forms: the possible morphologies of predicted common ancestors”:
http://www.talkorigins.org/faqs/comdesc/section1.html#morphological_intermediates

Note that their figures show changes in existing features mixed with miraculous appearances of new features. Not feeling the need to address where these new features came from, they just add them when needed, and they ALWAYS appear fully formed and functional. (Begin with Figure 1.4.1)

Using TalkOrigins own criteria, let’s review how common descent holds up when using the Scientific Method of testing an hypothesis:

Make observations.
Form a testable, unifying hypothesis to explain these observations:
“By ‘testable,’ we mean the predictions must include examples of what is likely be observed if the hypothesis is true and of what is unlikely to be observed if the hypothesis is true. A hypothesis that can explain all possible data equally well is not testable, nor is it scientific. A good scientific hypothesis must rule out some conceivable possibilities, at least in principle.”
Deduce predictions from the hypothesis.
Search for confirmations of the predictions; if the predictions are contradicted by empirical observation, go back to step (2).
(From: http://www.talkorigins.org/faqs/comdesc/sciproof.html)
1. Observations:

There is NO direct observation of common descent:

“It is not necessarily easy to “see” macroevolutionary history; there are no firsthand accounts to be read. Instead, we reconstruct the history of life using multiple lines of evidence, including geology, fossils, and living organisms.”
http://evolution.berkeley.edu/evolibrary/article/_0_0/evoscales_05
2 & 3. There are NO testable, unifying hypotheses because there are NO exclusive and consistent predictions:

For an excellent overview of falsified Darwinian predictions, go to “Darwin’s Predictions”:
http://www.darwinspredictions.com/

a. The Theory of Evolution predicted that new genes were necessary to create more complex features in existing organisms. However, it has been discovered that lower forms of life already possess the genetic “toolkit” needed to cause more complex features to arise in higher forms of life:

“It is the underlying genetic tool kit that is similar amongst these basal animals. Placozoa have all of the tools in their genome to make a nervous system, but they just don’t do it.”
http://www.physorg.com/news152259480.html
“Another fascinating fact is sea urchins don’t have eyes, ears or a nose, but they have the genes humans have for vision, hearing and smelling …
Despite having no eyes, nose, or ears, the creature has genes involved in vision, hearing and smell in humans.”
http://www.sciencedaily.com/videos/2007/0304-sea_urchins_reveal_medical_mysteries.htm
“The findings reported in the August 21 online edition of the journal Nature show that while Trichoplax has one of the smallest nuclear genomes found in a multi-cellular creature, it contains signature sequences for gene regulation found in more complex animals and humans.”
http://www.sciencedaily.com/releases/2008/09/080903172419.htm
“Another surprise came from a complexity of components of the immune system in sea urchin. In addition to an extremely well developed system of the innate immunity, these animals possess genes encoding major components of the adaptive immune response … Yet, sea urchin does not have antibodies, and possibly lacks adaptive immunity in general. Genes that are seemingly useless in sea urchin but are very useful in higher taxons exemplify excessive genetic information in lower taxons.”
http://www.machanaim.org/philosof/nauka-rel/universal_genome.htm
“Long before animals with limbs (tetrapods) came onto the scene about 365 million years ago, fish already possessed the genes associated with helping to grow hands and feet (autopods) report University of Chicago researchers …
The capability of building limbs with fingers and toes existed for a long period of time, but it took a set of environmental triggers to make use of that capability…
“It had the tools,’ he said, “but it needed the opportunity as well.””
http://www.scientificblogging.com/news/new_genetic_data_overturns_
long_held_theory_of_limb_development
b. The Theory of Evolution predicts that life began as simple organisms, but complexity has been rule, not exception, in the earliest known fossils:

“Part of the intrigue with the Cambrian explosion is that numerous animal phyla with very distinct body plans arrive on the scene in a geological blink of the eye, with little or no warning of what is to come in rocks that predate this interval of time.”
http://www.ncbi.nlm.nih.gov/pubmed/19472371
“One of the most interesting challenges facing paleobiologists is explaining the Cambrian explosion, the dramatic appearance of most metazoan animal phyla in the Early Cambrian, and the subsequent stability of these body plans over the ensuing 530 million years.”
Kevin J. Peterson, Michael R. Dietrich, Mark A. McPeek, “MicroRNAs and macroevolution: insights into canalization, complexity, and the Cambrian Explosion,” (Hypothesis) Department of Biological Sciences, Dartmouth College
http://www.dartmouth.edu/~peterson/46-Bioessays.pdf
“Two paleontologists studying ancient fossils they excavated in the South Australian outback argue that Earth’s ecosystem has been complex for hundreds of millions of years – … Until now, the dominant paradigm in the field of paleobiology has been that the earliest multicellular animals were simple, and that strategies organisms use today to survive, reproduce and grow in numbers have arisen over time due to several factors … “How Funisia appears in the fossils clearly shows that ecosystems were complex very early in the history of animals on Earth – “”
http://www.sciencedaily.com/releases/2008/03/080320150025.htm
c. There are NO predictions or explanations for the appearance of a molecular structure called a primary cilium, which projects from the surface of most, if not all cells. It acts as a radio antenna that sends precise and essential instructions to the inner cell via frequency modified vibrations, i.e. sound waves.
How they originated and where the instructions come from (God) is impossible to address through secular science. Evolutionists have yet to propose a reasonable explanation:

“Despite the impressive amount of progress made over the past decade, we are left with even more challenging and critical questions. These questions include how extracellular stimuli perceived by the cilia result in changes in cell behavior and physiology …”
http://ajprenal.physiology.org/cgi/content/full/289/6/F1159
“The primary cilium, the solitary, antenna-like structure that studs the outer surfaces of virtually all human cells, orient cells to move in the right direction and at the speed needed to heal wounds, much like a Global Positioning System helps ships navigate to their destinations.”
http://www.physorg.com/news148742058.html
“The puzzle of how higher animals develop – how a mass of undifferentiated cells organise themselves into specialised, functioning tissues, organs, and organisms – could now be solved – and the clue has been right under our noses for over a century.
Every mammalian cell has a single primary cilium. This structure sticks out from the cell membrane like a cellphone aerial. First noticed by 19th Century microscopists, it was thought to be a useless, vestigial structure like the appendix. But recent discoveries show it is absolutely pivotal in cell differentiation and maintenance of tissue and organ structure and function.”
http://scimednet.blogspot.com/2008/06/primary-cilium-antenna-for-organising.html
“Almost every vertebrate cell has a specialized cell surface projection called a primary cilium. Although these structures were first described more than a century ago, the full scope of their functions remains poorly understood. Here, we review emerging evidence that in addition to their well-established roles in sight, smell, and mechanosensation, primary cilia are key participants in intercellular signaling.”
http://www.sciencemag.org/cgi/content/abstract/313/5787/629
d. There are NO predictions or explanations for the appearance of highly complex regulatory networks and control systems:

“The researchers found that blood cells are directed by a multitude of transcription factors, proteins that turn on and off genes … The findings point to densely, interconnected circuits that control this process, suggesting that the wiring for blood cell fate is far more complex than previously thought.”
Broad Institute of MIT and Harvard, “Global View of Blood Cell Development Reveals New and Complex Circuitry”, January 20, 2011, ScienceDaily.
http://www.sciencedaily.com/releases/2011/01/110120124957.htm
“Molecular motors, the little engines that power cell mobility and the ability of cells to transport internal cargo, work together and in close coordination, according to a new finding by researchers at the University of Virginia …
The new University of Virginia study provides strong evidence that the motors are indeed working in coordination, all pulling in one direction, as if under command, or in the opposite direction — again, as if under strict instruction.”
University of Virginia, “Molecular Motors In Cells Work Together, Study Shows,” February 25, 2009. http://www.sciencedaily.com/releases/2009/02/090213161043.htm
“FANTOM4 has shown that instead of having one or a few ‘master regulator’ genes that control growth and development, there is a sophisticated network of regulatory elements that subtly influence the ways in which genes are expressed in different cells in the body,” Professor John Mattick said.
University of Queensland, “Study Challenges Notions Of How Genes Are Controlled In Mammals,” April 23, 2009. http://www.sciencedaily.com/releases/2009/04/090420103549.htm
“Had Amin Rustom not messed up, he would not have stumbled upon one of the biggest discoveries in biology of recent times …
Using video microscopy, they watched adjacent cells reach out to each other with antenna-like projections, establish contact and then build the tubular connections. The connections were not just between pairs of cells. Cells can send out several nanotubes, forming an intricate and transient network of linked cells lasting anything from minutes to hours.
… Nothing in his experience could explain the phenomenon.”
“Tunnelling nanotubes: Life’s secret network,” New Scientist, November 18, 2008.
http://www.newscientist.com/article/mg20026821.400-tunnelling-nanotubes-lifes-secret-network.html
“The scientists found out that the new electrical signal they called “system potential” was induced and even modulated by wounding. If a plant leaf is wounded, the signal strength can be different and can be measured over long distances in unwounded leaves, depending on the kind and concentration of added cations (e.g. calcium, potassium, or magnesium). It is not the transport of ions across cell membranes that causes the observed changes in voltage transmitted from leaf to shoot and then to the next leaf, but the activation of so-called proton pumps.”
Justus Liebig University of Gießen and the Max Planck Institute for Chemical Ecology in Jena,“Novel Electric Signals In Plants Induced By Wounding Plant,” March 10, 2009.
http://www.sciencedaily.com/releases/2009/03/090309105030.htm
“The p53 protein, which exists in all the cells of the body, is commonly called the “guardian of the genome”, since it detects harmful DNA changes and prevents them from being transmitted further into the body. p53 activates genetic programmes that arrest the division and growth of damaged cells or trigger their apoptosis. In half of all cancer tumours, the gene for p53 is damaged, and the scientists believe that the protein has been rendered dysfunctional in all cancer tumours.”
Karolinska Institutet, Stockholm, Sweden, “New research on the ‘guardian of the genome,’”May 12, 2009, PhyOrg.com website.
http://www.physorg.com/news161360881.html
e. The Theory of Evolution predicts that organisms become more complex throughout time, but some become less complex, and some never change at all:

“A new and comprehensive analysis confirms that the evolutionary relationships among animals are not as simple as previously thought. The traditional idea that animal evolution has followed a trajectory from simple to complex—from sponge to chordate—meets a dramatic exception in the metazoan tree of life.”
http://www.physorg.com/news152259480.html
“If you start with the simplest possible animal body, then there’s only one direction to evolve in – you have to become more complex, …”
http://www.physorg.com/news124992599.html
“The second is that the sponge evolved its simpler form from the more complex form. This second possibility underscores the fact that “evolution is not necessarily just a march towards increased complexity,” Dunn said.””
http://www.livescience.com/animals/080410-first-animal.html
“Just as tetrapods went off and did something crazy with their fin by adding to it, zebrafish went off and did something crazy by losing part of their fin.”
http://www.scientificblogging.com/news/new_genetic_data_overturns_
long_held_theory_of_limb_development
“Coelacanths are well known from the fossil record of 75 million to 400 million years ago … Coelacanths fascinate because of their unusual appearance and evolutionary importance. They have remained virtually unchanged morphologically for millions of years, leading some to call them “living fossils.””
http://www.flmnh.ufl.edu/fish/InNews/fossil2004.html
“These simply organized organisms do not have specialized muscle or nerve cells and nevertheless survived the last 500 million years almost unchanged and are considered a link between the single-cell dominated Precambrian and later multicellular organisms.”
http://www.sciencedaily.com/releases/2009/10/091016224153.htm
f. The Theory of Evolution predicts that accumulations of genetic change will eventually produce profound changes in organisms. However, inheritable genetic alterations have never created more complexity because most copying errors are ‘re-written’ by miniscule machines, and alterations that proceed to the next generation most often produce less fit organisms:

“Research published in 2007 showed the importance of the nuclear protein UHRF1 in ensuring that the epigenetic code is accurately copied …
The key element of UHRF1 involved in this “proofreading” process is known as the Set and Ring Associated (SRA) domain, but the exact mechanisms by which the SRA domain accomplishes this task were unclear.”
http://www.sciencedaily.com/releases/2008/09/080903134159.htm
“A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order …
The authors sought to identify the underlying cause for this self-correcting behavior in the observed protein chains. Standard evolutionary theory offered no clues … The scientists are working on formulating a new general theory based on this finding they are calling “evolutionary control.””
http://www.physorg.com/news145549897.html
“In short, the notion that molecules of germ cells … are in states of perpetual change is not, in our present understanding of cell biology, tenable. This doesn’t mean that “molecular change” does not occur; only that mechanisms provoking such change in germ cells are likely instantaneous and stochastic and probably often lethal (Maresca and Schwartz 2006) – which will preclude their persistence into future generations.”
http://www.mitpressjournals.org/doi/abs/10.1162/biot.2006.1.4.357
“Alterations in the normal recombination pattern are often associated with errors in chromosome segregation in humans, and these errors are a major cause of spontaneous abortions and congenital birth defects, including mental retardation.”
(Go to “Meiotic Recombination Does Not Occur at Random Throughout the Genome”)
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.
pbio.0050333&ct=1&SESSID=a273f04ca1957b1da05dfd35ba0c418a
g. The Theory of Evolution predicted that once genetic changes were ‘fixed’ in populations, previous DNA would not arise again. However, it has been shown that organisms can miraculously restore DNA up to 200 millions of years in a frog and 8 generations in plants AFTER a feature has disappeared:

“Gastrotheca guentheri, one of a group of frogs known for carrying fertilized eggs in pouches, is the only ranine species known for sporting teeth on both upper and lower jaws. That trait is unusual because frogs are said to have been missing their lower teeth for some 200 million years.
For that reason, the quirk represents an apparent violation of Dollo’s Law, which states that traits that disappear in the course of evolution will never return. Study leader John Wiens explained, ‘The loss of mandibular teeth in the ancestor of modern frogs and their re-appearance in G. guentheri provides very strong evidence for the controversial idea that complex anatomical traits that are evolutionarily lost can re-evolve, even after being absent for hundreds of millions of years.’”
University of Kansas, “Frogs Re-evolved Lost Lower Teeth”, January 31, 2011, BBC News.
http://news.bbc.co.uk/earth/hi/earth_news/newsid_9365000/9365076.stm
“Here we show that Arabidopsis plants homozygous for recessive mutant alleles of the organ fusion gene HOTHEAD5 (HTH) can inherit allele-specific DNA sequence information hat was not present in the chromosomal genome of their parents but was present in previous generations. This previously undescribed process is shown to occur at all DNA sequence polymorphisms examined and therefore seems to be a general mechanism for extra-genomic inheritance of DNA sequence information. We postulate that these genetic restoration events are the result of a template-directed process that makes use of an ancestral RNA-sequence cache.”
http://www.nature.com/nature/journal/v434/n7032/abs/nature03380.html
“Here, we show that a rice triploid and diploid hybridization resulted in stable diploid progenies, both in genotypes and phenotypes, through gene homozygosity. Furthermore, their gene homozygosity can be inherited through 8 generations, and they can convert DNA sequences of other rice varieties into their own. Molecular-marker examination confirmed that this type of genome-wide gene conversion occurred at a very high frequency. Possible mechanisms, including RNA-templated repair of double-strand DNA, are discussed.”
http://www.ncbi.nlm.nih.gov/pubmed/17502903?ordinalpos=1&itool=EntrezSystem2.
PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_Discovery_RA
h. The Theory of Evolution predicts that related organisms will share the same genes and similar features (homology), but unrelated organisms share the same genes and possess almost identical features (convergent evolution):

“Biologists have shown that independent but similar molecular changes turned a harmless digestive enzyme into a toxin in two unrelated species — a shrew and a lizard — giving each a venomous bite.
… “It’s remarkable that the same types of changes have independently promoted the same toxic end product.””
http://www.sciencedaily.com/releases/2009/10/091029125532.htm
“About one-quarter of apid bees are so-called cleptoparasitic bees, which secretly invade host nests and lay their eggs there. The new study reports that these bees did not independently evolve from nest-making bees 11 times over history, as bee experts have reported for years, but independently evolved only four times.”
http://www.physorg.com/news203616637.html
“Animals that seem identical may belong to completely different species. This is the conclusion of researchers at the University of Gothenburg, Sweden, who have used DNA analyses to discover that one of our most common segmented worms is actually two types of worm. The result is one of many suggesting that the variety of species on the earth could be considerably larger than we thought …
But when the researchers examined the worms using advanced methods for DNA analysis, they discovered that they were in fact two different species. Both species of worm differ in one of the examined genes by 17 percent, which is twice as much as the equivalent difference between humans and chimpanzees.”
http://www.physorg.com/news159631527.html
“This means that the nervous system, once thought to have arisen once, must have evolved twice from the DNA that coded for these complex systems (keeping in mind that while Placozoans and sponges do not have nervous systems, many of the taxa related to them do.)
DeSalle agrees. “It is the underlying genetic tool kit that is similar amongst these basal animals. Placozoa have all of the tools in their genome to make a nervous system, but they just don’t do it.””
http://www.physorg.com/news152259480.html
“A team led by Jay Storz (prounounced storts), assistant professor of biological sciences, analyzed the complete genome sequences of multiple vertebrate species and found that jawless fishes (e.g., lampreys and hagfish) and jawed vertebrates (pretty much everything else, including humans) independently invented different mechanisms of blood-oxygen transport to sustain aerobic metabolism.”
http://www.physorg.com/news199440678.html
“The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off.”
http://news.nationalgeographic.com/news/2007/05/070510-opossum-dna.html
“Flying squirrels and sugar gliders are only distantly related. So why do they look so similar then? Their gliding “wings” and big eyes are analogous structures. Natural selection independently adapted both lineages for similar lifestyles: leaping from treetops (hence, the gliding “wings”) and foraging at night (hence, the big eyes).”
http://evolution.berkeley.edu/evolibrary/article/0_0_0/analogy_02
“Elephant shrews were originally classified as shrews (Soricidae) because of a superficial resemblance. However, in the late 1990s, when biologists began using detailed information on genetic sequences to reconstruct the family tree of mammals, the results were surprising. Elephant shrews were not closely related to shrews or to other mammal groups like rabbits, with which they had sometimes been lumped. Instead, the elephant shrew twig sprang from an unexpected branch of the tree: the aardvark, manatee, and elephant lineage!”
http://evolution.berkeley.edu/evolibrary/news/080301_elephantshrew
i. The Theory of Evolution predicts that DNA sequencing would establish firm branches in family trees, but it has only added more confusion:

“Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: “For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality.” …
Dr Dupré said: “It’s part of a revolutionary change in biology. Our standard model of evolution is under enormous pressure. We’re clearly going to see evolution as much more about mergers and collaboration than change within isolated lineages.””
“Charles Darwin’s tree of life is ‘wrong and misleading’, claim scientists”, January 22, 2009, Telegraph UK Online.
http://www.telegraph.co.uk/science/4312355/Charles-Darwins-tree-of-life-is-wrong-and-misleading-claim-scientists.html
“Today’s computational tools use sequence similarity, assuming that genes with similar sequences indicate common ancestry … But Durand’s tests showed that this assumption often does not hold. Her team found disturbing results when they compared sequence similarity to their Neighborhood Correlation method in evaluating the 20 gene families with established histories. The sequence similarity method actually yielded false ancestral associations and missed true ancestral relationships.”
http://www.sciencedaily.com/releases/2008/05/080515205640.htm
j. The Theory of Evolution predicts that fossils can be accurately dated, but new research shows the inconsistency of dating techniques:

“The precise timing of the origin of life on Earth and the changes in life during the past 4.5 billion years has been a subject of great controversy for the past century. The principal indicator of the amount of organic carbon produced by biological activity traditionally used is the ratio of the less abundant isotope of carbon, 13C, to the more abundant isotope, 12C.
It appears that records related to carbonate platforms which are often used throughout the early history of the Earth are not good recorders of the 13C/12C ratio in the open oceans. Hence, the work presented suggests that assumptions made previously about changes in the 13C/12C ratios of carbonate sediments in the geological record are incorrect.”
http://www.physorg.com/news140266859.html
“But in biological systems, there is a small bias in the use of each isotope (called “fractionation”) which results in biological tissues having a different ratio of 12C to 13C than the ‘wild’ carbon floating around, say, in the atmosphere …
It turns out that a study of these different depositional environments, in the paper by Swart, indicates that the two data sources behave differently and the non-ocean bottom deposits cannot be used as they previously were. As a result of this, our understanding of the history of the Earth’s carbon cycle has gone all topsy-turvy and now needs to be re-examined.”
http://scienceblogs.com/gregladen/2008/09/warning_will_robinson_warning.php
k. The Theory of Evolution predicts that molecular and fossil dating will be consistent, but inconsistencies are the rule, not the exception:

“Therefore, we conclude that dating ages of origin of taxa with molecular phylogenetic trees where fossils are used as calibration points, is, at best, ambiguous (e.g, Sanderson 1997: Thorne & Kishino 2002).”
“Temporal paralogy, cladograms, and the quality of the fossil record” Publications Scientifiques du Museum national d’Histoire naturelle, Paris, Geodiversitas, 2004, 26 (3) (See PDF)
“In line with our model, molecular evolution trees often do not fit a morphology-based evolution tree.”
http://www.machanaim.org/philosof/nauka-rel/universal_genome.htm
l. The Theory of Evolution predicts that fossils can be dated by their position within layers of the earth (strata), but layers do not reflect a uniform geological column. In fact, marine fossil remains (limestone) have been found on top of EVERY mountain range in the world:

“I hope I have convinced you that the sedimentary record is largely a record of episodic events rather than being uniformly continuous. My message is that episodicity is the rule, not the exception…. We need to shed those lingering subconscious constraints of old uniformitarian thinking.”
(Emeritus) Professor Robert Dott, Sedimentary Geology, UW Madison, “The Rule”, Presidential Address To Society of Economic Paleontologists & Mineralogists, Geotimes, Nov. 1982, p.16 Dott is a co-author of a leading textbook of earth history, Evolution of the Earth (McGraw-Hill), which is now in its 7th edition. In 1995, he received the Geological Society of America’s History of Geology Division Award.
“Relative dating places fossils in a temporal sequence by noting their positions in layers of rocks, known as strata … Sometimes this method doesn’t work, either because the layers weren’t deposited horizontally to begin with, or because they have been overturned.”
http://evolution.berkeley.edu/evolibrary/article/0_0_0/lines_10
“Earth movements over extremely long periods of earth’s history can lift limestone miles into the air. The summit of Mount Everest is limestone that started out on an ocean floor.”
http://www.granitech.net/faq.htm
m. The Theory of Evolution predicts that evolution is still occurring, but there are no isolated populations emerging that reflect new organs or body parts forming. Regardless of the excuses, documentation of observable macroevolution is non-existent:

“It is not necessarily easy to “see” macroevolutionary history; there are no firsthand accounts to be read. Instead, we reconstruct the history of life using multiple lines of evidence, including geology, fossils, and living organisms.”
http://evolution.berkeley.edu/evolibrary/article/_0_0/evoscales_05
4. All predictions are contradictory, so none of the hypotheses of evolution are testable and, therefore, the hypothesis of common descent (macroevolution) cannot be confirmed.

REVIEW WHAT IS CONSIDERED ‘NATURALISTIC’ (SCIENTIFIC) BY EVOLUTIONARY STANDARDS:

“In science, explanations must be based on naturally occurring phenomena. Natural causes are, in principle, reproducible and therefore can be checked independently by others.”
“Science, Evolution, and Creationism,” 2008, National Academy of Sciences (NAS), The National Academies Press, third edition, page 10.
http://www.nap.edu/openbook.php?record_id=11876&page=10
1. Are there any mechanisms that have been proven to create new features or structures in existing organisms, as well as ones that are a “naturally occurring phenomena”?

a. See the inability of evolutionists to describe how common descent supposedly occurs:

http://pub17.bravenet.com/forum/1424646898/fetch/756950/
http://pub17.bravenet.com/forum/1424646898/fetch/748021/
http://pub17.bravenet.com/forum/1424646898/fetch/746941/
http://pub17.bravenet.com/forum/1424646898/fetch/730697/
http://pub17.bravenet.com/forum/1424646898/fetch/730410/
Also, go to http://www.whoisyourcreator.com/how_does_evolution_occur.html
b. See how evolutionists even openly admit to NOT knowing how evolution supposedly occurs:

“Students should realize that although virtually all scientists accept the general concept of evolution of species, scientists do have different opinions on how fast and by what mechanisms evolution proceeds.”
The American Association for the Advancement of Science, Educational Benchmarks, (F) Evolution of Life
http://www.project2061.org/publications/bsl/online/ch5/ch5.htm#F
“Scientists are still uncovering the specifics of how, when, and why evolution produced the life we see on Earth today.”
Smithsonian’s National Museum of Natural History
http://www.nmnh.si.edu/paleo/geotime/main/foundation_life3.html
“But they are trying to figure out how evolution happens, and that’s not an easy job.”
University of California Museum of Paleontology and the National Center for Science Education
http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_50
“Precisely how and at what rates descent with modification occurs are areas of intense research. For example, much work is under way testing the significance of natural selection as the main driving force of evolution.”
The American Geological Institute
http://www.agiweb.org/news/evolution/mechanismforchange.html
2. Is common descent “reproducible and therefore can be checked independently by others”?
With all the thousands of experiments with bacteria, fruit flies, and other organisms, scientists have yet to create or see any hint of common descent:

“Throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another …
Since there is no evidence for species changes between the simplest
forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms.”
Alan H. Linton, University of Bristol bacteriologist, in an April, 2001 article entitled “Scant Search for the Maker” Times Higher Education Supplement, 2001.
http://www.jodkowski.pl/ke/ALinton.html
“Despite a close watch, we have witnessed no new species emerge in the wild in recorded history. Also, most remarkably, we have seen no new animal species emerge in domestic breeding. That includes no new species of fruit flies in hundreds of millions of generations in fruit fly studies, where both soft and harsh pressures have been deliberately applied to the fly populations to induce speciation…we also clearly see that the limits of variation appear to be narrowly bounded, and often bounded within species.”
Kevin Kelly, Board Chair and founder of the ALL Species Foundation, in his book, “Out of Control”: The New Biology of Machines” 1994, Fourth Estate:London, 1995, reprint, p.475. ALL Species Foundation is a non-profit organization dedicated to the complete inventory, including describing and classifying, all of the species of life on Earth by 2025.
Results:
Since there is NO proof that common descent (macroevolution) is a “naturally occurring phenomena” or is “reproducible and therefore can be checked independently by others,” ALL existing evolutionary explanations for common descent (macroevolution) MUST be given the correct status of being supernatural, i.e. something attributed to a power that seems to violate or go beyond natural forces.

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Common descent

The dramatic divergence of bacteriophage genomes is an
obstacle that frequently prevents the detection of homology
between proteins and, thus, the determination of phylogenetic
links between phages. 1

http://reasonandscience.heavenforum.org/t1615-common-descent

“DR ROSE SAID: ‘THE TREE OF LIFE IS BEING POLITELY BURIED – WE ALL KNOW
THAT. WHAT’S LESS ACCEPTED IS OUR WHOLE FUNDAMENTAL VIEW OF BIOLOGY NEEDS
TO CHANGE.’ HE SAYS BIOLOGY IS VASTLY MORE COMPLEX THAN WE THOUGHT AND FACING UP TO THIS COMPLEXITY WILL BE
AS SCARY AS THE CONCEPTUAL UPHEAVALS PHYSICISTS HAD
TO TAKE ON BOARD IN THE EARLY 20TH CENTURY.”



The Telegraph UK, “Charles Darwin’s tree of life is ‘wrong and misleading’ claim scientists,” January 22, 2009.

http://www.telegraph.co.uk/science/4312355/Charles-Darwins-tree-of-life-is-wrong-and-misleading-claimscientists.html

http://www.uncommondescent.com/genetics/new-mechanism-of-evolution-poof/

Each species has large numbers of unique genes that seem to have magically arisen without any ancestor. Evolutionists are saying they essentially POOFed into existence. These genes are referred to as ORFans or orphan genes. From the Max Plank Institute:

with the advent of sequencing of full genomes, it became clear that approximately 20–40% of the identified genes could not be associated with a gene family that was known before. Such genes were originally called ‘orphan’ genes

20-40% of the genes discovered cannot be explained by common ancestry or common descent. So what mechanism is left to explain it? Special creation? But evolutionists can’t accept special creation, so they just pretend they’ve made a discovery of a new mechanism of evolution that can work just as well. They haven’t given it a name yet, so let us call it POOF. What is POOF? POOF is the mechanism by which proteins can easily arise out random nucleotide sequences like a poem can emerge out of randomly tossed scrabble letters. I bold one of their euphemisms for the POOF mechanism in the following paragraph:

Orphan genes may have played key roles in generating lineage specific adaptations and could be a continuous source of evolutionary novelties. Their existence suggests that functional ribonucleic acids (RNAs) and proteins can relatively easily arise out of random nucleotide sequences, although these processes still need to be experimentally explored.

The reasoning they use goes like this, “we have all these genes that can’t be explained by slight successive modifications, so they must have arisen spontaneously out of nowhere. Because evolution is fact, this implies evolution can just take random material and create functional systems in a flash. We’ve made a fabulous discovery about the miracles of evolution even though we can’t demonstrate it experimentally.”

Experiments actually refute such assertions, but that won’t stop evolutionists from promoting demonstrably false ideas as some new discovery! And it’s not only the genes but the regulatory mechanisms that poof into existence:

On the other hand, there is now little doubt that new genes have arisen throughout the phylogenetic history and the general model of de novo evolution of genes appears to be well supported by now. However, this also raises several new questions. The foremost one is the question of how new promotors with a defined regulation can arise.

“de novo evolution of genes” is also another euphemism for the POOF mechanism.

But it’s not just the genes and regulatory regions, but also developmental mechanisms that deploy these novelties to create radical new species (like multicellular ones from single cellular ones).

gene lists can be associated with major evolutionary steps, such as the origin of germ layers, or the origin of multicellularity . Interestingly, this approach showed also that younger genes tend to be increasingly more developmentally regulated compared with evolutionary older genes



http://news.nationalgeographic.com.au/news/2010/05/100513-science-evolution-darwin-single-ancestor/

http://scienceblogs.com/neurophilosophy/2009/07/03/evolutionary-origins-of-the-nervous-system/

vertebrates, worms and insects are all believed to be descended from a common ancestor – a worm-like organism, named Urbilateria


http://www.uncommondescent.com/evolution/icc-2013-paul-nelsons-keynote-address/

even if a pair of organisms are 90% similar, that 10% difference could be sufficient to falsify common ancestry if the gap in differences are sufficiently large to be bridged by mindless processes.

IF it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.

   Charles Darwin

So how much difference is needed to challenge common descent? Consider if you had 90% of the characters correct in a 5000 character cryptographic key, is it reasonable to assume chance processes will resolve the final 10%? It is probably very easy to make a biological organism 10% different from another in terms of destructive processes, but not so easy in terms of constructive process since new protein systems are like new login/password, lock-and-key systems.

Common Ancestry: Wikipedia vs. the Data

Does the molecular data give evidence of common ancestry? Representing a common view among Darwinian evolutionists, Wikipedia says yes: "Universal biochemical organization and molecular variance patterns in all organisms also show a direct correlation with common descent." Did you get that? -- "all organisms"! To show why this statement is wildly false, I could give numerous examples to the contrary. Let's consider two:

First, consider a recent paper in Annual Review of Genetics which observes that huge percentages of eukaryotic genes do not show a "direct correlation with common descent," but rather tell directly conflicting stories about supposed phylogenetic history. Here's a recreation of Table 2 from the paper:

Eukaryotic genes and their closest prokaryotic relative.
Closest eukaryotic relative Percent of total
Cyanobacteria 15.3
Alphaproteobacteria 8.5
Gammaproteobacteria 6.3
Betaproteobacteria 2.3
Probable proteobacteria 8.4
Other bacteria 12.8
Archae 9.6
No prokaryotic homolog 36.6

(From Table 2, Michael Syvanen, "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, Vol. 46:339-356 (2012).)

This table shows that eukaryotic genes send extremely mixed messages about the supposedly closest prokaryotic relative of eukaryotes. (Of course "closest prokaryotic relative" merely means "which prokaryote's version of a gene has the highest sequence similarity to the eukaryotic version of the gene?") Some eukaryote genes are most similar to one type of prokaryote, whereas other eukaryote genes are most similar to another. There's no consensus from eukaryote genes about eukaryote ancestry.

In fact, the largest category of genes here is eukaryotic genes that have no homolog among prokaryotes -- they don't even have any possible candidate ancestors to explain where these genes came from, much less a consistent pattern of similarity pointing to one particular ancestor. All this is the opposite of "a direct correlation with common descent."

Darwinian evolutionists will try to retain common descent and explain away this data by ad hoc appeals to horizontal gene transfer (HGT), or by inventing hypothetical ancestors as needed to donate these homologue-lacking genes. In fact, this paper explains that evolutionary biologists typically treat phylogenetic conflicts as a very "test" for the presence of HGT:

   The classic test for inferring HGT is the phylogenetic congruency test, whereby a gene tree is compared with a species tree (or possibly some other reference tree made up of different genes) and the question is posited: Are the two topologies different and is the difference significant?

   (Michael Syvanen, "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, Vol. 46:339-356 (2012).)

In other words, if two phylogenetic trees aren't congruent, the problem isn't that common descent is wrong, but rather the conflict is simply evidence of HGT. Let me put it another way: most evolutionary biologists do not treat common descent in a scientific fashion where it is capable of being falsified. If the data doesn't fit with common ancestry, they simply take that as evidence for ad hoc fallback explanations like HGT. Syvanen invokes widespread HGT, but he's uncommonly honest about the data and its implications, offering the radical suggestion that "life might indeed have multiple origins."

Regardless, one thing is clear: this data does not show that "Universal biochemical organization and molecular variance patterns in all organisms also show a direct correlation with common descent." If there was such a "direct correlation with common descent," then they wouldn't be resorting to invoking HGT.

Second, let's now look within eukaryotes. Can biochemical similarities between plants and animals be explained by common ancestry? It turns out that they have a highly similar biochemical organization of their respective innate immune systems, but their common ancestor didn't have an innate immune system. Common descent cannot explain these "unexpectedly similar" systems. Consider these striking comments from a paper in Nature Immunology:

   "Although it seems to be generally accepted that the innate immune responses of plants and animals share at least some common evolutionary origins, examination of the available data fails to support that conclusion, despite similarities in the overall 'logic' of the innate immune response in diverse multicellular eukaryotes."

   "Although the underlying logic of multicellular development in plants and animals is unexpectedly similar, it seems that multicellularity evolved independently in plants and animals and that the basic molecular mechanisms specifying pattern formation were independently derived."

   "Although adaptive immunity is unique to vertebrates, the innate immune response seems to have ancient origins. Common features of innate immunity in vertebrates, invertebrate animals and plants include defined receptors for microbe-associated molecules, conserved mitogen-associated protein kinase signaling cascades and the production of antimicrobial peptides. It is commonly reported that these similarities in innate immunity represent a process of divergent evolution from an ancient unicellular eukaryote that pre-dated the divergence of the plant and animal kingdoms. However, at present, data suggest that the seemingly analogous regulatory modules used in plant and animal innate immunity are a consequence of convergent evolution and reflect inherent constraints on how an innate immune system can be constructed."

   (Frederick M Ausubel, "Are innate immune signaling pathways in plants and animals conserved?," Nature Immunology, Vol. 6 (10): 973-979 (October, 2005) (internal citations omitted).)

The biochemical organization of the innate immune systems of plants and animals is strikingly similar -- but this is a direct non-correlation with common descent. Under their evolutionary thinking, these are forced to call the systems "unexpectedly similar," postulating that the similarities were "independently derived." This type of data is neither anticipated nor explained by Darwinian evolution and common descent. It is anticipated and explained by common design.

http://www.judgingpbs.com/dfp-slide9.html

The nice, neat, nested hierarchy of a grand Tree of Life predicted by Darwinian theory has not been found. Evolutionary biologists are increasingly appealing to epicycles like horizontal gene transfer, differing rates of evolution, abrupt molecular radiation, convergent evolution (even convergent molecular evolution), and other ad hoc rationalizations to reconcile discrepancies between phylogenetic hypothesis. Darwinian biology is not explaining the molecular data; it is forced to explain away the data. PBS paints a rosy picture of the data, when the data isn't good news for Darwinism.

Are Rotifers Gene Stealers or Uniquely Engineered?

http://designed-dna.org/blog/files/category-microbial-oddities.php

The tools of DNA sequencing are becoming cheaper to use and more productive than ever, and the deluge of DNA comparison results between organisms coming forth are becoming a quagmire for the evolutionary paradigm. To prop it up, biologists resort to ever more absurd explanations for discrepancies. A prime example of this trickery is in a recent DNA sequencing project performed in a microscopic aquatic multi-cellular animal called a rotifer .

In this effort, the researchers targeted those gene sequences that are expressed as proteins for DNA sequencing because the genome was too large and complex to sequence and assemble all of its DNA.

Are Rotifers Gene Stealers or Uniquely Engineered?


http://reasonandscience.heavenforum.org/t1615-common-descent?highlight=common


They recorded over 61,000 gene sequences that were expressed from rotifers grown in stressed and non-stressed conditions. Of these, they could only find sequence similarities between rotifers and other creatures for 28,922 sequences (less than half). The researchers tossed the unknown DNA sequences out of their analysis since the non-similar genes were novel, apparently specific to rotifer, and essentially difficult for evolution to explain.

Of the 28,922 sequences for which they could obtain a match in a public database of other creature's DNA and protein sequences, a significant proportion (more than in any other creature sequenced) did not fit evolutionary expectations of common descent. Further complicating this picture, the rotifer gene sequences were found in a diverse number of non-rotifer creatures!


Some of the creatures that had gene matches to rotifers included a variety of plants, other multicellular animals, protists (complex single celled animals), archaea, bacteria, and fungi.

Evolutionists have two options in which to categorize these unusual gene matches based on their naturalistic presuppositions. First, they can say that these genes evolved independently in separate creatures in a hypothetical process called "convergent evolution." However, in cases where there are literally hundreds of these DNA sequences popping up in multiple organisms, this scenario becomes so unlikely that even evolutionists have too much difficulty imagining it. The second option is called "horizontal gene transfer," or HGT. This involves the transfer of genes, perhaps via some sort of microbial host vector such as a bacterium (2).

In the present report, the rotifer under study was asexual, limiting heredity as an option for aiding in gene transfer. So the researchers concluded that it stole hundreds of genes via HGT from a plethora of other creatures.

HGT is considered somewhat common among bacteria because they form connective tubes (called pili) and exchange little bits of DNA, like sharing software. Also, HGT can occur rarely between a bacterium and a multicellular host that it interacts with during its life cycle .

How will rotifer researchers account for the massive transfer of hundreds of genes from a broad range of hosts that they believe includes 533 supposed source genomes for which no biological host-based relationships exists? Some sort of causal host relationship must occur for the transfer of one gene, let alone hundreds of genes from hundreds of sources .

Another problem is that the researchers showed that the so-called "stolen genes" were well-integrated into the rotifer cell biochemistry and its environmental adaptation mechanisms. A separate 2012 study showed that highly expressed native genes could not be shared via HGT, even among bacteria, because they would severely disrupt essential cell biochemistry . And these are exactly the types of genes that were surveyed in the rotifer.

In this case, evolutionary biologists have resorted to fictional stories cloaked in technical terminology to escape the straightforward conclusion that rotifer DNA was purposefully crafted. If a large bunch of newly discovered genes don't make evolutionary sense, then evolution proponents ascribe their origin to HGT despite the fact that HGT is not known to operate without any host-based relationship. HGT is also not known to occur en masse, and HGT of essential genes is in theory impossible .

The unique mix of rotifer genes along with their flawless biochemical integration into the rotifer's cell system, clearly and abundantly supports the special creation described in the Bible.

Common Descent? - Some Insurmountable Problems (for gradualism and/or transformation)

“Evolution, in the sense of common descent, is not a theory of similarity. Linnaeus, Cuvier, and Agassiz knew all about similarity, yet they denied common descent. Evolution is a theory of transformation.”,,,
Paul Nelson - What Evolution Is, and What It's Not - October 30, 2015
http://www.evolutionnews.org/2015/10/what_evolution100501.html

To highlight why the approach of appealing to mutations to DNA is ‘not even wrong’ in regards to explaining how the unique human ‘form’ came about, no one has EVER even changed one creature into another creature by mutations to DNA as is presupposed in neo-Darwinian thought:

‘No matter what we do to a fruit fly embryo there are only three possible outcomes, a normal fruit fly, a defective fruit fly, or a dead fruit fly. What we never see is primary speciation much less macro-evolution’ –
Jonathan Wells
Darwin’s Theory – Fruit Flies and Morphology – video
http://www.youtube.com/watch?v=hZJTIwRY0bs

Response to John Wise – October 2010
Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html

“While it may be an adequate scenario for the refinement of some already-existing characters — the beaks of finches, color intensity of moths — the “microevolutionary” process envisioned by Darwin and his successors does not account in any plausible way for “macroevolutionary” patterns such as the differences between oysters and grasshoppers, fish and birds. ”
~ Stuart Newman, “Where do complex organisms come from.”

Nor, despite the fact that Darwinists claim their theory is on par with gravity, has anyone ever even seen one creature change into another creature:

Scant search for the Maker
Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms.
– Alan H. Linton – emeritus professor of bacteriology, University of Bristol.
http://www.timeshighereducation.co.uk/story.asp?storycode=159282

A review of The Edge of Evolution: The Search for the Limits of Darwinism
The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
http://creation.com/review-michael-behe-edge-of-evolution

Natural Selection and Evolution’s Smoking Gun, – American Scientist – 1997
Excerpt: “A matter of unfinished business for biologists is the identification of evolution’s smoking gun,”…
“Perhaps the most obvious challenge is to demonstrate evolution empirically. There are, arguably, some 2 to 10 million species on earth. The fossil record shows that most species survive somewhere between 3 and 5 million years. In that case, we ought to be seeing small but significant numbers of originations (new species) .. every decade.”
(“the smoking gun of evolution is speciation, not local adaptation and differentiation of populations.”)
Keith Stewart Thomson, Professor of Biology and Dean of the Graduate School, Yale University (Nov. -Dec. American Scientist, 1997 pg. 516)
http://www.jstor.org/stable/27856885?seq=1#page_scan_tab_contents

“The closest science has come to observing and recording actual speciation in animals is the work of Theodosius Dobzhansky in Drosophilia paulistorium fruit flies. But even here, only reproductive isolation, not a new species, appeared.”
from page 32 “Acquiring Genomes” Lynn Margulis.

Selection and Speciation: Why Darwinism Is False – Jonathan Wells – 2009
Excerpt: there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another.”
http://www.evolutionnews.org/2009/05/selection_and_speciation_why_d.htm l

Meyers puts the one of the primary reasons why mutations to DNA cannot change one creature into another creature like this

‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’
Stephen Meyer – (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate – 2009) (52:57 minute mark)
https://youtu.be/7yqqlZ29gcU?t=3177

Jonathan Wells recently wrote some papers highlighting many of those higher levels of information, that are above the DNA coding, that Dr. Meyer alluded to in his debate with Shermer and Prothero:

Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA – Jonathan Wells – 2014
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.2/BIO-C.2014.2

podcast – Dr. Jonathan Wells explains the concept of codes in living things, and how they affect the debate over neo-Darwinism and intelligent design. (at least 5 different codes in life besides the genetic code) – Oct. 2015
http://www.discovery.org/multimedia/audio/2015/10/id-inquiry-jonathan-wells-on-codes-in-biology/#more-31141

Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information – Jonathan Wells – published online May 2013
Conclusion:,, Recent discoveries of multiple overlapping functions in non-protein-coding DNA show that the biological information in the genome far exceeds that in the protein-coding regions alone. Yet biological information is not limited to the genome. Even at the level of gene expression – transcription and translation — the cell must access information that is not encoded in DNA. Many different RNAs can be generated from a single piece of DNA by alternative splicing, and although some splicing codes occur in intronic DNA there is no empirical justification for assuming that all of the information for tissue- and developmental-stage-specific alternative splicing resides in DNA.,, even after RNA has specified the amino acid sequence of a protein, additional information is needed: Protein function depends on three-dimensional shape, and the same sequence of amino acids can be folded differently to produce proteins with different three-dimensional shapes [144–147]. Conversely, proteins with different amino acid sequences can be folded to produce similar shapes and functions [148,149]. Many scientists have pointed out that the relationship between the genome and the organism – the genotype-phenotype mapping – cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. So non-protein-coding regions of DNA that some previously regarded as “junk” turn out to encode biological information that greatly increases the known information-carrying capacity of DNA. At the same time, DNA as a whole turns out to encode only part of the biological information needed for life.
http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0009

1) http://mmbr.asm.org/content/75/3/423.full.pdf

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Besides there being overlapping coding that are, hierarchically, above the coding of DNA, we find that there also is overlapping coding within DNA as well:

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].
http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006

“There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns – which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture – which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes).
Dr. John Sanford; Genetic Entropy 2005

Moreover, there are very good mathematical reasons why overlapping coding within DNA will prevent one creature from ever being changed into another creature.

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
Conclusions: Our analysis confirms mathematically what would seem intuitively obvious – multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006

A very simple way to understand the monumental brick wall any evolutionary scenario faces with the multiple overlapping coding found in DNA is with the following puzzle found on page 141 of the book ‘Genetic Entropy’ by Dr. Sanford.

S A T O R
A R E P O
T E N E T
O P E R A
R O T A S

Which is translated ;

THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS.

This ancient puzzle, which dates back to at least 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation (save for the center).
This is what is meant when it is said that a poly-functional genome is poly-constrained to any random mutations.
This poly-constrained principle is why we never see the unlimited plasticity in organisms that was, and is, imagined by Darwin and his followers, and is also why random mutations, that have effects that great enough that we are able to measure them, are almost always deleterious in the effects that are measured:

“Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.”
R. Milner, Encyclopedia of Evolution (1990)

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – May 2013
Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11].
1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696.
2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19.
3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358.
4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144.
5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47.
6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117.
8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526.
9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685.
10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079.
11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006

Moreover, at the morphological and behavioral level we find that Chimps and Humans are far more different than is commonly believed.
In fact, King and Wilson, who were the first ones to suggest that we are 98% similar to chimps at the genetic level, said that since the morphological and behavioral disparity between chimps and humans is so great then the morphological and behavioral disparity between humans and apes must be due to variations in their genomic regulatory systems since such similarity in the protein coding regions obviously could not explain that great morphological and behavioral disparity between chimps and humans.

In “Science,” 1975, M-C King and A.C. Wilson were the first to publish a paper estimating the degree of similarity between the human and the chimpanzee genome. This documented the degree of genetic similarity between the two! The study, using a limited data set, found that we were far more similar than was thought possible at the time. Hence, we must be one with apes mustn’t we? But…in the second section of their paper King and Wilson honestly describe the deficiencies of such reasoning:
“The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than sibling species in anatomy and way of life. Although humans and chimpanzees are rather similar in the structure of the thorax and arms, they differ substantially not only in brain size but also in the anatomy of the pelvis, foot, and jaws, as well as in relative lengths of limbs and digits (38).
Humans and chimpanzees also differ significantly in many other anatomical respects, to the extent that nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart (38).
Associated with these anatomical differences there are, of course, major differences in posture (see cover picture), mode of locomotion, methods of procuring food, and means of communication. Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families (39). So it appears that molecular and organismal methods of evaluating the chimpanzee human difference yield quite different conclusions (40).”

King and Wilson went on to suggest that the morphological and behavioral between humans and apes,, must be due to variations in their genomic regulatory systems.
David Berlinski – The Devil’s Delusion – Page 162&163
Evolution at Two Levels in Humans and Chimpanzees Mary-Claire King; A. C. Wilson – 1975
http://academic.reed.edu/biology/professors/srenn/pages/teaching/BIO431S05_2008/431S05_readings/431s05_examples/king_wilson_1975(classic)

In fact, so great are the anatomical differences between humans and chimps that a Darwinist, since pigs are anatomically closer to humans than chimps are, actually proposed that a chimp and pig mated with each other and that is what ultimately gave rise to humans. (I guess even hybridization knows no limits in the minds of some Darwinists).
Moreover, Physorg published a subsequent article showing that the pig-chimp hybrid theory for human origins is much harder to shoot down than some other Darwinists, who opposed McCarthy’s radical theory, had first supposed it would be:

Human hybrids: a closer look at the theory and evidence – July 25, 2013
Excerpt: There was considerable fallout, both positive and negative, from our first story covering the radical pig-chimp hybrid theory put forth by Dr. Eugene McCarthy,,,By and large, those coming out against the theory had surprisingly little science to offer in their sometimes personal attacks against McCarthy.
,,,Under the alternative hypothesis (humans are not pig-chimp hybrids), the assumption is that humans and chimpanzees are equally distant from pigs. You would therefore expect chimp traits not seen in humans to be present in pigs at about the same rate as are human traits not found in chimps. However, when he searched the literature for traits that distinguish humans and chimps, and compiled a lengthy list of such traits, he found that it was always humans who were similar to pigs with respect to these traits. This finding is inconsistent with the possibility that humans are not pig-chimp hybrids, that is, it rejects that hypothesis.,,,
http://phys.org/news/2013-07-human-hybrids-closer-theory-evidence.html

Of course there is not one single scrap of empirical evidence that suggests that such radically different creatures, such as pigs and chimps, could ever successfully produce viable offspring.
But alas, when your theory is built on storytelling in the first place, (and not on any real empirical evidence), then of course you are not going to be able to shoot down another ‘just so story’ just because you don’t like how the narrative contradicts your preferred narrative of man ascending from monkeys:

“We have all seen the canonical parade of apes, each one becoming more human. We know that, as a depiction of evolution, this line-up is tosh (i.e. nonsense). Yet we cling to it. Ideas of what human evolution ought to have been like still colour our debates.”
Henry Gee, editor of Nature (478, 6 October 2011, page 34, doi:10.1038/478034a),

In further note to King and Wilson’s observation that ‘nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart’, this observation by King and Wilson, by itself, places another severe constraint on the Darwinian evolution that, once again, calls the entire theory into question.
Simply put, since nearly every bone is readily distinguishable between chimps and humans, then multiple simultaneous coordinated changes are required instead of just individual changes, as is envisioned in Darwinism, so as to prevent catastrophic results:

K´necting The Dots: Modeling Functional Integration In Biological Systems – June 11, 2010
Excerpt: “If an engineer modifies the length of the piston rods in an internal combustion engine, but does not modify the crankshaft accordingly, the engine won’t start. Similarly, processes of development are so tightly integrated temporally and spatially that one change early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream” (1)
http://www.uncommondescent.com/intelligent-design/k%C2%B4necting-the-dots-modeling-functional-integration-in-biological-systems/

“This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create….
(Quoted in “Discover Interview: Lynn Margulis Says She’s Not Controversial, She’s Right,” Discover Magazine, p. 68 (April, 2011).)

“The real number of variations is lesser than expected,,. There are no blue-eyed Drosophila, no viviparous birds or turtles, no hexapod mammals, etc. Such observations provoke non-Darwinian evolutionary concepts. Darwin tried rather unsuccessfully to solve the problem of the contradictions between his model of random variability and the existence of constraints. He tried to hide this complication citing abundant facts on other phenomena. The authors of the modern versions of Darwinism followed this strategy, allowing the question to persist. …However, he was forced to admit some cases where creating anything humans may wish for was impossible. For example, when the English farmers decided to get cows with thick hams, they soon abandoned this attempt since they perished too frequently during delivery. Evidently such cases provoked an idea on the limitations to variability… [If you have the time, read all of the following paper, which concludes] The problem of the constraints on variation was not solved neither within the framework of the proper Darwin’s theory, nor within the framework of modern Darwinism.” (IGOR POPOV, THE PROBLEM OF CONSTRAINTS ON VARIATION, FROM DARWIN TO THE PRESENT, 2009,
http://www.ludusvitalis.org/textos/32/32-11_popov.pdf

Perhaps that is why so many engineers support intelligent design since they can readily see the impossibility of the ‘engineering problem’ for Darwinian processes. Namely, Design must be implemented top down, with all the pieces coordinated with one another, so as to avoid catastrophic results for the system as a whole.
Moreover, in further note to King and Wilson’s contention that the morphological and behavioral disparity between humans and apes must be due to variations in their genomic regulatory systems, (since the genetic similarity obviously cannot explain that great morphological and behavioral disparity between chimps and humans), we find that it is indeed in the genetic regulatory regions that we find ‘orders of magnitude’ and ‘species specific’ differences between not only chimps and humans, but also in other species as well:
Just a reminder, genetic similarity is far more widespread, across very different species, than Darwinists expected the genetic similarity to be

Shark and human proteins “stunningly similar”; shark closer to human than to zebrafish – December 9, 2013
Excerpt: “We were very surprised to find, that for many categories of proteins, sharks share more similarities with humans than zebrafish,” Stanhope said. “Although sharks and bony fishes are not closely related, they are nonetheless both fish … while mammals have very different anatomies and physiologies.
http://www.uncommondescent.com/intelligent-design/shark-and-human-proteins-stunningly-similar-shark-closer-to-human-than-to-zebrafish/

Kangaroo genes close to humans
Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,”
http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118

First Decoded Marsupial Genome Reveals “Junk DNA” Surprise – 2007
Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,,
The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off.
http://news.nationalgeographic.com/news/2007/05/070510-opossum-dna.html

Where could we have learned but from Phys.org – Sept. 28, 2014
Excerpt: “We have basically the same 20,000 (30,000?) protein-coding genes as a frog, yet our genome is much more complicated, with more layers of gene regulation.”
http://www.uncommondescent.com/human-evolution/where-could-we-have-learned-but-from-phys-org/

Yet it is exactly in these genetic regulatory networks that ‘orders of magnitude’ differences are found between species:

Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F

Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013
Excerpt: Although humans and chimpanzees share,, similar genomes, previous studies have shown that the species evolved major differences in mRNA (messenger RNA) expression levels.,,,
http://www.sciencedaily.com/releases/2013/10/131017144632.htm

“Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes.”
Raymond Bohlin (per Richard Sternberg) – 9:29 minute mark of video
http://www.metacafe.com/watch/8593991/

On Human Origins: Is Our Genome Full of Junk DNA? Pt 2. – Richard Sternberg PhD. Evolutionary Biology
Excerpt: “Here’s the interesting thing, when you look at the protein coding sequences that you have in your cell what you find is that they are nearly identical to the protein coding sequences of a dog, of a carp, of a fruit fly, of a nematode. They are virtually the same and they are interchangeable. You can knock out a gene that encodes a protein for an inner ear bone in say a mouse. This has been done. And then you can take a protein that is similar to it but from a fruit fly. And fruit flies aren’t vertebrates and they certainly are not mammals., so they don’t have inner ear bones. And you can plug that gene in and guess what happens? The offspring of the mouse will have a perfectly normal inner ear bone. So you can swap out all these files. I mentioning this to you because when you hear about we are 99% similar (to chimps) it is almost all referring to those protein coding regions. When you start looking, and you start comparing different mammals. Dolphins, aardvarks, elephants, manatees, humans, chimpanzees,, it doesn’t really matter. What you find is that the protein coding sequences are very well conserved, and there is also a lot of the DNA that is not protein coding that is also highly conserved. But when you look at the chromosomes and those banding patterns, those bar codes, (mentioned at the beginning of the talk), its akin to going into the grocery store. You see a bunch of black and white lines right? You’ve seen one bar code you’ve seen them all. But those bar codes are not the same.,, Here’s an example, aardvark and human chromosomes. They look very similar at the DNA level when you take small snippets of them. (Yet) When you look at how they are arranged in a linear pattern along the chromosome they turn out to be very distinct (from one another). So when you get to the folder and the super-folder and the higher order level, that’s when you find these striking differences. And here is another example. They are now sequencing the nuclear DNA of the Atlantic bottle-nose dolphin. And when they started initially sequencing the DNA, the first thing they realized is that basically the Dolphin genome is almost wholly identical to the human genome. That is, there are a few chromosome rearrangements here and there, you line the sequences up and they fit very well. Yet no one would argue, based on a statement like that, that bottle-nose dolphins are closely related to us. Our sister species if you will. No one would presume to do that. So you would have to layer in some other presumption. But here is the point. You will see these statements throughout the literature of how common things are.,,, (Parts lists are very similar, but how the parts are used is where you will find tremendous differences)
http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-2/

Moreover, unlike protein coding regions where there is some ‘non-catastrophic’ tolerance to random mutations, randomly mutating gene regulatory networks is found to be ‘always catastrophically bad':

A Listener’s Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin – December 4, 2013
Excerpt: “There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.” –
Eric Davidson – developmental biologist
http://www.evolutionnews.org/2013/12/a_listeners_gui079811.html

Thus, where Darwinists most need plasticity in the genome to be viable as a theory, (i.e. developmental Gene Regulatory Networks), is the place where mutations are found to be ‘always catastrophically bad’. Yet, it is exactly in this area of the genome (i.e. regulatory networks) where substantial, ‘orders of magnitude’, differences are found between even supposedly closely related species.
Needless to say, this is the exact opposite finding for what Darwinism would have predicted for what should have been found in the genome.
If Darwinism were a normal science, instead of being basically the unfalsifiable ‘blind faith’ religion of atheists, this finding, by itself, should have been more than enough to falsify neo-Darwinian claims.

Of supplemental note to Richard Sternberg’s ‘bar codes are not the same’ between species quote. It turns out that the bar code pattern that Dr. Sternberg alluded to is irreducibly complex in its organizational relation to the individual genes:

Refereed scientific article on DNA argues for irreducible complexity – October 2, 2013
Excerpt: This paper published online this summer is a true mind-blower showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc.,,
,,,First, the digital information of individual genes (semantics) is dependent on the the intergenic regions (as we know) which is like analog information (syntax). Both types of information are co-dependent and self-referential but you can’t get syntax from semantics. As the authors state, “thus the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organizational complexity of the genetic regulation system of any cell”. In short, the linear DNA sequence contains both types of information. Second, the paper links local DNA structure, to domains, to the overall chromosome configuration as a dynamic system keying off the metabolic signals of the cell. This implies that the position and organization of genes on the chromosome is not arbitrary,,, http://www.christianscientific.org/refereed-scientific-article-on-dna-argues-for-irreducibly-complexity/

This has been a fairly long post, (even for me Smile ), but hopefully for the open minded person who is honestly trying to see if either ID or Darwinism is true, this post has made it abundantly clear that neo-Darwinian explanations are grossly deficient on several different levels as to explaining the amazing integrated complexity we see in life, and that ID explanations are, by far, the most satisfactory explanations for that amazing integrated complexity that we see.

complementary notes:

Contrary to popular belief, the fossil record certainly, when looked at in its entirety, does not support the hypothesis of common descent,

(Disparity consistently precedes diversity in the fossil record)
disparity
[dih-spar-i-tee] noun, plural disparities.
1. lack of similarity or equality; inequality; difference:
http://www.uncommondescent.com/intelligent-design/double-debunking-glenn-williamson-on-human-chimp-dna-similarity-and-genes-unique-to-human-beings/#comment-585067

In fact, the ‘argument from form’ also gives us very good evidence that we each must have a soul so as to explain how the billion-trillion protein molecules of a human body can possibly cohere as a single unified whole for ‘precisely a lifetime, and not a moment longer’ (Talbott).
http://www.uncommondescent.com/intelligent-design/double-debunking-glenn-williamson-on-human-chimp-dna-similarity-and-genes-unique-to-human-beings/#comment-585035

Body plans, contrary to neo-Darwinian presuppositions, simply are not reducible to DNA, period! That finding pretty much renders any Darwinian argument for common ancestry based on DNA alone moot and void:
http://www.uncommondescent.com/intelligent-design/double-debunking-glenn-williamson-on-human-chimp-dna-similarity-and-genes-unique-to-human-beings/#comment-584415

A Big Problem for Common Descent: Hundreds of "Active 'Foreign' Genes" Don't Fit the Standard Evolutionary Phylogeny
http://www.evolutionnews.org/2015/03/a_big_problem_f094701.html

Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth
http://www.hindawi.com/journals/tswj/2012/479824/

A Primer on the Tree of Life
http://www.ideacenter.org/contentmgr/showdetails.php/id/1481

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